From 4a03254f4d76b77e61d7d7e4b91f18875cf24827 Mon Sep 17 00:00:00 2001 From: GuyTeichman <48219633+GuyTeichman@users.noreply.github.com> Date: Fri, 5 Jan 2024 16:09:04 +0200 Subject: [PATCH] updated release description --- HISTORY.rst | 7 ++++++- docs/build/.doctrees/environment.pickle | Bin 849824 -> 863433 bytes docs/build/.doctrees/history.doctree | Bin 233432 -> 234282 bytes docs/build/history.html | 8 ++++++-- docs/build/index.html | 2 +- docs/build/searchindex.js | 2 +- 6 files changed, 14 insertions(+), 5 deletions(-) diff --git a/HISTORY.rst b/HISTORY.rst index 9556ecb0..3579902a 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -2,8 +2,13 @@ History ======= -3.11.0 (2024-01-04) +3.11.0 (2024-01-05) ------------------- +This release brings several exciting new features. +Notably, these inclue the ability to run functions from the Picardtools suite, and the ability to automatically save interactive session reports and later resume them from any saved session. +In addition, this release includes several visual upgrades, bug fixes, and quality-of-life improvements. +Happy analysis! + Added ******* * *RNAlysis* can now run functions from the Picardtools suite, including conversion functions (BAM to SAM, SAM to FASTQ, FASTQ to SAM, etc), quality control (validate SAM), and post-processing functions (remove PCR duplicates, sort SAM, create BAM index). diff --git a/docs/build/.doctrees/environment.pickle b/docs/build/.doctrees/environment.pickle index cd6996dee6e76f1facbe938602334fa24ba897ad..9ac3d1460c0255a823982c3bd731c33d11f62f18 100644 GIT binary patch literal 863433 zcmeFadAuA&)jxb8WZx6WPBL%_BtY)X24NM#5{N*EB!Ei7Fn6Z!o$1V$S#EN{fPe^r z27(MCDk`G5>%*o3q9P(7@}MFrE{_i?iXteY_~6ESPMz+qs_yEknp^Px{?X6#kaMTc zsXpIYPMtb+s`{NHZ`h-2w=VpjH?3aH7s}gvobq6yRwdT5YZK#^oy6M$K_@g<8uy`h+7kozxskZ*&UTd?{1jw0#wfmD4{9~Qo;$1kDY@&I+nmnzgJ0^4UtczcA49Ci-B4 zzegQU4?^w7RtB9~t&nr-0LB~VY;QQ_dZALTw>AT|ur9VYdNR#M1vG4VGlB~8f2=o4 zrA%$8C2=Dbr`~8e-smcUZh2z@)Gcppwo)Cc6$bK9x6_s{UB2w#6x3HLs4qYOugh1U 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Change history:

  • History
      -
    • 3.11.0 (2024-01-04)
        +
      • 3.11.0 (2024-01-05)
        • Added
        • Changed
        • Fixed
          • @@ -280,7 +280,11 @@

          History

          -

          3.11.0 (2024-01-04)

          +

          3.11.0 (2024-01-05)

          +

          This release brings several exciting new features. +Notably, these inclue the ability to run functions from the Picardtools suite, and the ability to automatically save interactive session reports and later resume them from any saved session. +In addition, this release includes several visual upgrades, bug fixes, and quality-of-life improvements. +Happy analysis!

          Added

            diff --git a/docs/build/index.html b/docs/build/index.html index 2279c0c9..8592baa2 100644 --- a/docs/build/index.html +++ b/docs/build/index.html @@ -207,7 +207,7 @@

            RNAlysis 3.11.0 documentationChange history:

            • History
                -
              • 3.11.0 (2024-01-04)
                • +
              • 3.11.0 (2024-01-05)
              • 3.10.1 (2023-11-22)
              • 3.10.0 (2023-10-31)
              • 3.9.2 (2023-06-23)
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10, 109, 110, 112, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 156, 170, 350], "new": [0, 1, 2, 6, 10, 16, 19, 22, 23, 24, 25, 26, 30, 36, 37, 38, 39, 44, 46, 47, 54, 57, 60, 61, 62, 63, 64, 68, 74, 75, 76, 77, 85, 87, 88, 109, 110, 112, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 131, 140, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 156, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 188, 189, 191, 192, 193, 194, 195, 196, 199, 200, 201, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 229, 230, 231, 232, 233, 239, 240, 241, 244, 245, 246, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 271, 272, 273, 274, 275, 281, 282, 285, 286, 287, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 313, 314, 315, 316, 317, 319, 324, 326, 329, 330, 331, 335, 350], "each": [0, 2, 4, 5, 10, 14, 29, 35, 36, 37, 38, 39, 40, 49, 52, 67, 73, 74, 75, 76, 77, 78, 90, 94, 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307, 308, 313, 314, 315, 316, 324, 350, 351, 352], "determin": [0, 5, 9, 10, 14, 15, 22, 23, 25, 29, 35, 40, 46, 49, 52, 53, 60, 61, 63, 67, 73, 78, 82, 83, 84, 87, 90, 91, 94, 95, 109, 110, 111, 121, 124, 126, 132, 133, 134, 135, 141, 142, 143, 145, 149, 162, 163, 172, 175, 178, 179, 185, 192, 193, 194, 195, 196, 201, 203, 205, 206, 211, 212, 214, 217, 221, 228, 246, 248, 250, 251, 255, 256, 258, 261, 270, 287, 290, 291, 296, 297, 299, 302, 312, 331, 335, 350, 351, 352], "look": [0, 1, 2, 5, 6, 109, 110, 120, 121, 350, 351, 352], "involv": [0, 109, 110], "charact": [0, 5, 10, 109, 110, 124, 342, 343], "allow": [0, 1, 2, 5, 9, 10, 109, 110, 116, 117, 126, 127, 129, 192, 350, 351, 352], "clip": [0, 109, 110], "nucleotid": [0, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 46, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 87, 93, 109, 110, 124, 126, 127, 145, 146, 154, 155, 164, 165, 166, 167, 201, 214, 215, 223, 224, 229, 230, 231, 232, 246, 258, 259, 265, 266, 271, 272, 273, 274, 287, 299, 300, 307, 308, 313, 314, 315, 316, 331], "both": [0, 1, 4, 5, 7, 10, 29, 35, 36, 37, 38, 39, 44, 49, 67, 73, 74, 75, 76, 77, 82, 83, 84, 85, 90, 109, 110, 116, 126, 134, 141, 144, 164, 165, 166, 167, 178, 192, 197, 203, 213, 229, 230, 231, 232, 242, 257, 271, 272, 273, 274, 283, 298, 313, 314, 315, 316, 327, 350, 351, 352], "side": [0, 109, 110, 350, 352], "maxim": [0, 109, 110, 351, 352], "score": [0, 10, 27, 29, 35, 36, 39, 49, 65, 67, 73, 74, 77, 90, 91, 92, 109, 110, 116, 117, 118, 126, 127, 154, 164, 167, 223, 229, 232, 265, 271, 274, 307, 313, 316, 319, 350, 351, 352], "preset": [0, 109, 110], "higher": [0, 10, 109, 110, 193, 319, 350, 351, 352], "accur": [0, 1, 5, 109, 110, 351, 352], "take": [0, 5, 7, 9, 10, 39, 77, 94, 109, 110, 167, 192, 232, 274, 316, 350, 351, 352], "longer": [0, 5, 109, 110, 116], "calcul": [0, 5, 10, 19, 29, 30, 35, 39, 40, 44, 47, 49, 57, 67, 68, 73, 77, 78, 82, 83, 84, 85, 88, 90, 109, 110, 137, 156, 161, 163, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 178, 192, 193, 194, 195, 196, 197, 202, 208, 227, 228, 232, 242, 247, 253, 269, 270, 274, 283, 288, 289, 293, 311, 312, 316, 319, 327, 332, 350], "ignor": [0, 5, 10, 109, 110, 172, 175, 326, 351, 352], "qualiti": [0, 5, 109, 110, 116, 117, 118, 122, 123, 126, 127, 351, 352], "treat": [0, 5, 10, 109, 110, 124, 139], "them": [0, 1, 2, 5, 8, 10, 12, 29, 35, 49, 50, 67, 73, 82, 83, 84, 90, 109, 110, 116, 118, 122, 123, 126, 138, 139, 158, 159, 185, 248, 350, 351, 352], "maximum": [0, 10, 109, 110, 116, 118, 126, 127, 191, 194, 195, 196, 351], "encod": [0, 5, 109, 110], "most": [0, 1, 4, 5, 6, 10, 29, 35, 49, 67, 73, 82, 83, 84, 90, 109, 110, 179, 187, 190, 192, 193, 194, 195, 196, 350, 351, 352], "modern": [0, 109, 110], "setup": [0, 1, 2, 5, 7, 10, 109, 110, 192, 350], "phred": [0, 109, 110, 122, 123], "33": [0, 10, 39, 77, 109, 110, 136, 167, 207, 232, 252, 274, 292, 316], "minimum": [0, 10, 39, 77, 82, 83, 84, 109, 116, 117, 124, 126, 127, 167, 179, 192, 193, 232, 274, 316, 350, 351, 352], "fragment": [0, 109, 116, 117, 121, 350, 351], "length": [0, 10, 109, 116, 118, 119, 121, 153, 172, 175, 186, 222, 238, 264, 280, 306, 323, 350, 351, 352], "valid": [0, 5, 10, 39, 77, 83, 84, 109, 116, 124, 128, 130, 167, 204, 232, 274, 289, 316, 350, 351, 352], "seed": [0, 10, 29, 67, 109, 110, 111, 195, 196, 350, 351, 352], "pseudo": [0, 10, 39, 77, 109, 110, 111, 167, 169, 232, 274, 316], "random": [0, 5, 7, 10, 29, 35, 36, 37, 38, 39, 49, 67, 73, 74, 75, 76, 77, 90, 109, 110, 111, 118, 124, 139, 164, 165, 166, 167, 195, 196, 229, 230, 231, 232, 271, 272, 273, 274, 313, 314, 315, 316, 319, 350, 352], "number": [0, 4, 5, 9, 10, 14, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 46, 49, 52, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 78, 82, 83, 84, 87, 90, 91, 93, 109, 110, 111, 116, 117, 120, 121, 124, 126, 127, 132, 133, 145, 146, 150, 154, 155, 160, 164, 165, 166, 167, 168, 171, 177, 179, 191, 192, 193, 194, 195, 196, 198, 199, 201, 205, 206, 214, 215, 223, 224, 226, 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7, 10, 19, 36, 37, 38, 39, 57, 74, 75, 76, 77, 94, 95, 111, 116, 120, 121, 126, 137, 138, 139, 149, 153, 160, 161, 164, 165, 166, 167, 168, 169, 170, 171, 175, 179, 185, 186, 189, 191, 197, 208, 217, 222, 226, 227, 229, 230, 231, 232, 238, 240, 241, 242, 253, 261, 264, 268, 269, 271, 272, 273, 274, 280, 282, 283, 289, 293, 302, 306, 310, 311, 313, 314, 315, 316, 323, 325, 326, 327, 334, 350, 351, 352], "Be": [0, 111, 119], "awar": [0, 111, 119], "popular": [0, 111, 119, 350], "model": [0, 5, 9, 10, 111, 118, 119, 120, 121, 139, 350, 351, 352], "organ": [0, 5, 8, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 111, 119, 145, 146, 154, 155, 164, 165, 166, 167, 214, 215, 223, 224, 229, 230, 231, 232, 258, 259, 265, 266, 271, 272, 273, 274, 299, 300, 307, 308, 313, 314, 315, 316, 350], "These": [0, 5, 10, 11, 111, 116, 117, 119, 124, 350, 351, 352], "basenam": [0, 111], "creat": [0, 1, 5, 6, 9, 10, 111, 185, 192, 248, 335], "3": [0, 1, 2, 9, 10, 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350, 352], "denomin": [0, 5, 10, 138, 139, 156, 289, 295, 303, 309, 319, 326, 350, 351, 352], "differential_expression_limma_voom": [0, 5, 10], "random_effect": [0, 10, 139], "limma": [0, 5, 9, 10, 139, 171, 351, 352], "voom": [0, 5, 9, 10, 139], "effect": [0, 5, 10, 13, 51, 139, 192, 350, 351, 352], "drop": [0, 10, 36, 37, 38, 39, 46, 74, 75, 76, 77, 87, 130, 140, 164, 165, 166, 167, 201, 204, 209, 229, 230, 231, 232, 246, 249, 254, 271, 272, 273, 274, 287, 294, 313, 314, 315, 316, 331, 350, 352], "fro": [0, 10, 140, 209, 254, 294], "mthe": [0, 10, 140, 209, 254, 294], "enhanced_box_plot": [0, 5, 10], "enhanc": [0, 5, 10, 141], "rpm": [0, 10, 141, 150, 159, 173, 174, 185, 191, 351, 352], "filter_biotype_from_gtf": [0, 10], "lincrna": [0, 10, 22, 23, 60, 61, 142, 143, 211, 212, 255, 256, 296, 297, 351, 352], "ncrna": [0, 10, 22, 23, 60, 61, 142, 143, 211, 212, 255, 256, 296, 297], "pirna": [0, 10, 22, 23, 60, 61, 142, 143, 211, 212, 255, 256, 296, 297, 351, 352], "rrna": [0, 10, 22, 23, 60, 61, 142, 143, 211, 212, 255, 256, 296, 297], "snorna": [0, 10, 22, 23, 60, 61, 142, 143, 211, 212, 255, 256, 296, 297], "snrna": [0, 10, 22, 23, 60, 61, 142, 143, 211, 212, 255, 256, 296, 297], "trna": [0, 10, 22, 23, 60, 61, 142, 143, 211, 212, 255, 256, 296, 297], "anyth": [0, 1, 10, 22, 23, 24, 25, 26, 60, 61, 62, 63, 64, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 177, 199, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 233, 244, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 275, 285, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 317, 329, 350], "BUT": [0, 10, 22, 23, 24, 25, 26, 60, 61, 62, 63, 64, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 177, 199, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 233, 244, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 275, 285, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 317, 329], "expect": [0, 5, 10, 22, 23, 24, 25, 26, 29, 35, 40, 49, 60, 61, 62, 63, 64, 67, 73, 78, 82, 83, 84, 90, 91, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 177, 199, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 233, 244, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 275, 285, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 317, 319, 329, 350, 351, 352], "filter_biotype_from_ref_t": [0, 4, 5, 10, 319, 351], "defin": [0, 4, 5, 9, 10, 11, 23, 24, 29, 40, 49, 61, 62, 67, 78, 82, 83, 90, 94, 95, 143, 144, 179, 212, 213, 256, 257, 297, 298, 348, 349], "whose": [0, 5, 10, 143, 148, 150, 151, 152, 162, 170, 179, 210, 212, 219, 220, 221, 256, 262, 263, 295, 297, 305, 350, 351, 352], "13": [0, 10, 39, 77, 143, 167, 186, 194, 212, 232, 238, 256, 274, 280, 297, 316, 319, 323, 350, 351, 352], "filter_by_attribut": [0, 4, 5, 10, 319, 351], "attribute1": [0, 10, 144, 188, 213, 239, 257, 281, 298, 319, 324, 351, 352], "attr_ref_table_for_exampl": [0, 10, 144, 188, 213, 239, 257, 281, 298, 319, 324, 351], "7": [0, 1, 2, 6, 9, 10, 39, 77, 144, 152, 160, 167, 188, 189, 192, 213, 220, 226, 232, 239, 240, 257, 263, 268, 274, 281, 282, 298, 310, 316, 319, 324, 350, 351, 352], "OR": [0, 10, 144, 197, 213, 242, 257, 283, 298, 327], "attribute3": [0, 10, 144, 213, 257, 298, 351, 352], "AND": [0, 10, 144, 213, 257, 298], "19": [0, 6, 9, 10, 39, 77, 144, 167, 192, 213, 232, 257, 274, 298, 316, 351, 352], "don": [0, 2, 5, 7, 8, 10, 144, 213, 257, 298, 350, 351, 352], "filter_by_go_annot": [0, 5, 10], "go_id": [0, 10, 25, 63, 145, 214, 258, 299], "arabodopsi": [0, 10, 25, 26, 29, 35, 63, 64, 67, 73, 83, 84, 145, 146, 214, 215, 258, 259, 299, 300], "thaliana": [0, 10, 25, 26, 28, 29, 35, 37, 38, 39, 63, 64, 66, 67, 73, 75, 76, 77, 83, 84, 145, 146, 155, 165, 166, 167, 214, 215, 224, 230, 231, 232, 258, 259, 266, 272, 273, 274, 299, 300, 308, 314, 315, 316], "caenorhabd": [0, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 145, 146, 154, 155, 164, 165, 166, 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37, 38, 39, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 145, 146, 154, 155, 164, 165, 166, 167, 214, 215, 223, 224, 229, 230, 231, 232, 258, 259, 265, 266, 271, 272, 273, 274, 299, 300, 307, 308, 313, 314, 315, 316], "melanogast": [0, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 145, 146, 154, 155, 164, 165, 166, 167, 214, 215, 223, 224, 229, 230, 231, 232, 258, 259, 265, 266, 271, 272, 273, 274, 299, 300, 307, 308, 313, 314, 315, 316], "escherichia": [0, 10, 25, 26, 28, 29, 35, 37, 38, 39, 63, 64, 66, 67, 73, 75, 76, 77, 83, 84, 145, 146, 155, 165, 166, 167, 214, 215, 224, 230, 231, 232, 258, 259, 266, 272, 273, 274, 299, 300, 308, 314, 315, 316], "coli": [0, 10, 25, 26, 28, 29, 35, 37, 38, 39, 63, 64, 66, 67, 73, 75, 76, 77, 83, 84, 145, 146, 155, 165, 166, 167, 214, 215, 224, 230, 231, 232, 258, 259, 266, 272, 273, 274, 299, 300, 308, 314, 315, 316], "homo": [0, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 63, 64, 65, 66, 67, 73, 74, 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36, 37, 38, 39, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 93, 145, 146, 154, 155, 164, 165, 166, 167, 214, 215, 223, 224, 229, 230, 231, 232, 258, 259, 265, 266, 271, 272, 273, 274, 299, 300, 307, 308, 313, 314, 315, 316, 351, 352], "uniprotkb": [0, 8, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 46, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 87, 93, 145, 146, 154, 155, 164, 165, 166, 167, 201, 214, 215, 223, 224, 229, 230, 231, 232, 246, 258, 259, 265, 266, 271, 272, 273, 274, 287, 299, 300, 307, 308, 313, 314, 315, 316, 331, 351, 352], "ac": [0, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 46, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 87, 93, 145, 146, 154, 155, 164, 165, 166, 167, 201, 214, 215, 223, 224, 229, 230, 231, 232, 246, 258, 259, 265, 266, 271, 272, 273, 274, 287, 299, 300, 307, 308, 313, 314, 315, 316, 331], "uniparc": [0, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 46, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 87, 93, 145, 146, 154, 155, 164, 165, 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351, 352], "geneid": [0, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 46, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 87, 93, 145, 146, 154, 155, 164, 165, 166, 167, 201, 214, 215, 223, 224, 229, 230, 231, 232, 246, 258, 259, 265, 266, 271, 272, 273, 274, 287, 299, 300, 307, 308, 313, 314, 315, 316, 331], "kegg": [0, 5, 9, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 46, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 87, 93, 145, 146, 154, 155, 164, 165, 166, 167, 201, 214, 215, 223, 224, 229, 230, 231, 232, 246, 258, 259, 265, 266, 271, 272, 273, 274, 287, 299, 300, 307, 308, 313, 314, 315, 316, 331, 350], "patric": [0, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 46, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 87, 93, 145, 146, 154, 155, 164, 165, 166, 167, 201, 214, 215, 223, 224, 229, 230, 231, 232, 246, 258, 259, 265, 266, 271, 272, 273, 274, 287, 299, 300, 307, 308, 313, 314, 315, 316, 331], "ucsc": [0, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 46, 63, 64, 65, 66, 67, 73, 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313, 314, 315, 316, 331], "propagate_annot": [0, 10, 25, 29, 63, 67, 83, 145, 214, 258, 299], "evidence_typ": [0, 10, 25, 29, 63, 67, 83, 145, 214, 258, 299, 351, 352], "phylogenet": [0, 9, 10, 25, 29, 63, 67, 83, 145, 214, 258, 299, 351, 352], "author": [0, 10, 25, 29, 63, 67, 83, 145, 214, 258, 299, 351, 352], "curat": [0, 10, 25, 29, 35, 63, 67, 73, 83, 84, 145, 214, 258, 299, 350, 351, 352], "electron": [0, 10, 25, 29, 63, 67, 83, 145, 214, 258, 299, 351, 352], "excluded_evidence_typ": [0, 10, 25, 29, 63, 67, 83, 145, 214, 258, 299, 351, 352], "databas": [0, 5, 6, 9, 10, 25, 27, 28, 29, 36, 37, 38, 39, 63, 65, 66, 67, 74, 75, 76, 77, 83, 145, 154, 155, 164, 165, 166, 167, 214, 223, 224, 229, 230, 231, 232, 258, 265, 266, 271, 272, 273, 274, 299, 307, 308, 313, 314, 315, 316], "excluded_databas": [0, 10, 25, 29, 63, 67, 83, 145, 214, 258, 299, 351, 352], "qualifi": [0, 10, 25, 29, 63, 67, 83, 145, 214, 258, 299], "contributes_to": [0, 10, 25, 29, 63, 67, 83, 145, 214, 258, 299, 351, 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27, 36, 39, 65, 74, 77, 154, 164, 167, 223, 229, 232, 265, 271, 274, 307, 313, 316], "otu": [0, 10, 27, 36, 39, 65, 74, 77, 154, 164, 167, 223, 229, 232, 265, 271, 274, 307, 313, 316], "sunia": [0, 10, 27, 36, 39, 65, 74, 77, 154, 164, 167, 223, 229, 232, 265, 271, 274, 307, 313, 316], "ovi": [0, 10, 27, 36, 39, 65, 74, 77, 154, 164, 167, 223, 229, 232, 265, 271, 274, 307, 313, 316], "ari": [0, 10, 27, 36, 39, 65, 74, 77, 154, 164, 167, 223, 229, 232, 265, 271, 274, 307, 313, 316], "rambouillet": [0, 10, 27, 36, 65, 74, 154, 164, 223, 229, 265, 271, 307, 313], "pan": [0, 10, 27, 28, 36, 37, 38, 39, 65, 66, 74, 75, 76, 77, 154, 155, 164, 165, 166, 167, 223, 224, 229, 230, 231, 232, 265, 266, 271, 272, 273, 274, 307, 308, 313, 314, 315, 316], "paniscu": [0, 10, 27, 36, 39, 65, 74, 77, 154, 164, 167, 223, 229, 232, 265, 271, 274, 307, 313, 316], "troglodyt": [0, 10, 27, 28, 36, 37, 38, 39, 65, 66, 74, 75, 76, 77, 154, 155, 164, 165, 166, 167, 223, 224, 229, 230, 231, 232, 265, 266, 271, 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"wbgene": 351, "regular": 351, "graphic": 352, "workspac": 352, "gtf": 352, "summar": 352, "matrix": 352, "enabl": 352, "session": 352, "2024": 5, "convert_sam_format": 112, "create_bam_index": 113, "fastq_to_sam_pair": 114, "fastq_to_sam_singl": 115, "find_dupl": 118, "sam_to_fastq_pair": 122, "sam_to_fastq_singl": 123, "sort_sam": 125, "validate_sam": 128}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 57}, "alltitles": {"API Reference": [[0, "api-reference"]], "rnalysis.fastq module": [[0, "rnalysis-fastq-module"]], "rnalysis.filtering module": [[0, "rnalysis-filtering-module"], [10, "rnalysis-filtering-module"]], "rnalysis.enrichment module": [[0, "rnalysis-enrichment-module"], [10, "rnalysis-enrichment-module"]], "rnalysis.general module": [[0, "rnalysis-general-module"], [10, "rnalysis-general-module"]], "rnalysis.utils module": [[0, "rnalysis-utils-module"]], "How can I contribute to RNAlysis?": [[1, "how-can-i-contribute-to-rnalysis"]], "Types of Contributions": [[1, "types-of-contributions"]], "Report Bugs": [[1, "report-bugs"]], "Fix Bugs": [[1, "fix-bugs"]], "Write Documentation": [[1, "write-documentation"]], "Submit Feedback": [[1, "submit-feedback"]], "Implement Features": [[1, "implement-features"]], "Ideas/To-Do": [[1, "ideas-to-do"]], "RNAlysis Design Philosophy": [[1, "rnalysis-design-philosophy"]], "Get Started!": [[1, "get-started"]], "Pull Request Guidelines": [[1, "pull-request-guidelines"]], "Tips": [[1, "tips"]], "Deploying": [[1, "deploying"]], "Frequently asked questions": [[2, "frequently-asked-questions"]], "Installation": [[2, "installation"], [7, "installation"]], "I get an error message when I try to install RNAlysis. what can I do?": [[2, "i-get-an-error-message-when-i-try-to-install-rnalysis-what-can-i-do"]], "I get an error message when I try to install the RNAlysis hdbscan feature. what can I do?": [[2, "i-get-an-error-message-when-i-try-to-install-the-rnalysis-hdbscan-feature-what-can-i-do"]], "I get an error message when I try to install the RNAlysis randomization feature. what can I do?": [[2, "i-get-an-error-message-when-i-try-to-install-the-rnalysis-randomization-feature-what-can-i-do"]], "I am trying to open RNAlysis for the first time and it takes a long time to load/doesn\u2019t load at all. What should I do?": [[2, "i-am-trying-to-open-rnalysis-for-the-first-time-and-it-takes-a-long-time-to-load-doesn-t-load-at-all-what-should-i-do"]], "Can I install a previous version of RNAlysis?": [[2, "can-i-install-a-previous-version-of-rnalysis"]], "Usage": [[2, "usage"]], "I am trying to view the RNAlysis quick-start guide, but see only blank pages. What should I do?": [[2, "i-am-trying-to-view-the-rnalysis-quick-start-guide-but-see-only-blank-pages-what-should-i-do"]], "I am trying to apply a function to my data table. How do I know what all the different functions and parmeters do?": [[2, "i-am-trying-to-apply-a-function-to-my-data-table-how-do-i-know-what-all-the-different-functions-and-parmeters-do"]], "I want to use a particular statistical method or algorithm available in RNAlysis. How do I know exactly what it does and how it works?": [[2, "i-want-to-use-a-particular-statistical-method-or-algorithm-available-in-rnalysis-how-do-i-know-exactly-what-it-does-and-how-it-works"]], "What file formats are supported by RNAlysis?": [[2, "what-file-formats-are-supported-by-rnalysis"]], "What types of tables can I analyze with RNAlysis?": [[2, "what-types-of-tables-can-i-analyze-with-rnalysis"]], "When trying to run clustering/enrichment/other functions in RNAlysis, a progress bar appears but nothing happens. What can I do?": [[2, "when-trying-to-run-clustering-enrichment-other-functions-in-rnalysis-a-progress-bar-appears-but-nothing-happens-what-can-i-do"]], "I ran into a problem that is not specified here. What can I do?": [[2, "i-ran-into-a-problem-that-is-not-specified-here-what-can-i-do"]], "Automatic analysis reports": [[2, "automatic-analysis-reports"]], "How can I generate an analysis report?": [[2, "how-can-i-generate-an-analysis-report"]], "How can I view an analysis report?": [[2, "how-can-i-view-an-analysis-report"]], "How can I share an analysis report?": [[2, "how-can-i-share-an-analysis-report"]], "How can I access the data and figures that appear in an analysis report?": [[2, "how-can-i-access-the-data-and-figures-that-appear-in-an-analysis-report"]], "Do I need to generate analysis reports manually?": [[2, "do-i-need-to-generate-analysis-reports-manually"]], "Can I edit my analysis report?": [[2, "can-i-edit-my-analysis-report"]], "RNAlysis crashed during an analysis! Can I restore my automatic analysis report?": [[2, "rnalysis-crashed-during-an-analysis-can-i-restore-my-automatic-analysis-report"]], "Can I create an analysis report through the programmatic interface?": [[2, "can-i-create-an-analysis-report-through-the-programmatic-interface"]], "Index": [[3, "index"]], "Glossary - programmatic interface": [[4, "glossary-programmatic-interface"]], "History": [[5, "history"]], "3.11.0 (2024-01-04)": [[5, "id1"]], "Added": [[5, "added"], [5, "id3"], [5, "id6"], [5, "id13"], [5, "id17"], [5, "id22"], [5, "id28"], [5, "id32"], [5, "id38"], [5, "id49"], [5, "id55"], [5, "id62"], [5, "id71"], [5, "id75"], [5, "id80"], [5, "id86"], [5, "id90"], [5, "id94"], [5, "id98"], [5, "id105"]], "Changed": [[5, "changed"], [5, "id7"], [5, "id10"], [5, "id14"], [5, "id18"], [5, "id23"], [5, "id29"], [5, "id35"], [5, "id39"], [5, "id44"], [5, "id50"], [5, "id56"], [5, "id63"], [5, "id68"], [5, "id72"], [5, "id76"], [5, "id81"], [5, "id84"], [5, "id87"], [5, "id91"], [5, "id95"], [5, "id99"], [5, "id102"], [5, "id106"]], "Fixed": [[5, "fixed"], [5, "id4"], [5, "id8"], [5, "id11"], [5, "id15"], [5, "id19"], [5, "id24"], [5, "id30"], [5, "id33"], [5, "id36"], [5, "id40"], [5, "id45"], [5, "id47"], [5, "id51"], [5, "id53"], [5, "id57"], [5, "id64"], [5, "id66"], [5, "id69"], [5, "id73"], [5, "id77"], [5, "id82"], [5, "id88"], [5, "id92"], [5, "id96"], [5, "id100"], [5, "id103"], [5, "id107"]], "3.10.1 (2023-11-22)": [[5, "id2"]], "3.10.0 (2023-10-31)": [[5, "id5"]], "3.9.2 (2023-06-23)": [[5, "id9"]], "3.9.1 (2023-06-19)": [[5, "id12"]], "3.9.0 (2023-06-09)": [[5, "id16"]], "New Contributors": [[5, "new-contributors"], [5, "id26"], [5, "id42"], [5, "id60"]], "3.8.0 (2023-05-07)": [[5, "id21"]], "3.7.0 (2023-04-07)": [[5, "id27"]], "3.6.2 (2023-03-25)": [[5, "id31"]], "3.6.1 (2023-03-22)": [[5, "id34"]], "3.6.0 (2023-03-07)": [[5, "id37"]], "3.5.2 (2023-02-23)": [[5, "id43"]], "3.5.1 (2023-02-22)": [[5, "id46"]], "3.5.0 (2023-02-08)": [[5, "id48"]], "3.4.2 (2023-02-01)": [[5, "id52"]], "3.4.0 (2023-02-01)": [[5, "id54"]], "Removed": [[5, "removed"], [5, "id108"]], "3.3.0 (2022-12-02)": [[5, "id61"]], "3.2.2 (2022-11-25)": [[5, "id65"]], "3.2.1 (2022-11-25)": [[5, "id67"]], "3.2.0 (2022-11-23)": [[5, "id70"]], "3.1.0 (2022-10-16)": [[5, "id74"]], "3.0.1 (2022-10-12)": [[5, "id78"]], "3.0.0 (2022-10-10)": [[5, "id79"]], "2.1.1 (2022-07-05)": [[5, "id83"]], "2.1.0 (2022-04-16)": [[5, "id85"]], "2.0.1 (2022-04-02)": [[5, "id89"]], "2.0.0 (2021-12-05)": [[5, "id93"]], "1.3.5 (2020-05-27)": [[5, "id97"]], "1.3.4 (2020-04-07)": [[5, "id101"]], "1.3.3 (2020-03-28)": [[5, "id104"]], "1.3.2 (2019-12-11)": [[5, "id109"]], "RNAlysis 3.11.0 documentation": [[6, "rnalysis-release-documentation"]], "About RNAlysis:": [[6, null]], "Starting with RNAlysis:": [[6, null]], "Change history:": [[6, null]], "Modules:": [[6, "modules"]], "Indices and tables:": [[6, null]], "RNAlysis stand-alone app (most beginner-friendly)": [[7, "rnalysis-stand-alone-app-most-beginner-friendly"]], "How to install it": [[7, "how-to-install-it"], [7, "id1"], [7, "id3"]], "How to run it": [[7, "how-to-run-it"], [7, "id2"], [7, "id4"]], "Further guidance": [[7, "further-guidance"]], "Install as a Python package with pip (best performance)": [[7, "install-as-a-python-package-with-pip-best-performance"]], "From sources": [[7, "from-sources"]], "RNAlysis quick-start video guide": [[8, "rnalysis-quick-start-video-guide"]], "Open the program": [[8, "open-the-program"]], "Load a table": [[8, "load-a-table"]], "Examine your table": [[8, "examine-your-table"]], "Filter your table": [[8, "filter-your-table"]], "Undo the operations you applied to your table": [[8, "undo-the-operations-you-applied-to-your-table"]], "Apply your operations \u2018in-place\u2019 or apply on a new table": [[8, "apply-your-operations-in-place-or-apply-on-a-new-table"]], "Save the changes you made to your table": [[8, "save-the-changes-you-made-to-your-table"]], "Work on multiple tables at the same time": [[8, "work-on-multiple-tables-at-the-same-time"]], "Different types of tables offer different ways to filter and analyze your data": [[8, "different-types-of-tables-offer-different-ways-to-filter-and-analyze-your-data"]], "Create and save graphs": [[8, "create-and-save-graphs"]], "Quickly look-up genes in your database of choice": [[8, "quickly-look-up-genes-in-your-database-of-choice"]], "Sort your tabs and change their icons": [[8, "sort-your-tabs-and-change-their-icons"]], "Restore tabs you closed": [[8, "restore-tabs-you-closed"]], "Import lists of genes as Gene Sets": [[8, "import-lists-of-genes-as-gene-sets"]], "Visualize the intersections between your tables and gene sets": [[8, "visualize-the-intersections-between-your-tables-and-gene-sets"]], "Apply set operations to your tables and gene sets": [[8, "apply-set-operations-to-your-tables-and-gene-sets"]], "Perform enrichment analysis on your tables and gene sets": [[8, "perform-enrichment-analysis-on-your-tables-and-gene-sets"]], "Create Pipelines to streamline your data analysis": [[8, "create-pipelines-to-streamline-your-data-analysis"]], "Apply Pipelines to one or more of your tables": [[8, "apply-pipelines-to-one-or-more-of-your-tables"]], "Export and share Pipelines to make your analysis more reproducible": [[8, "export-and-share-pipelines-to-make-your-analysis-more-reproducible"]], "Interface with other bioinformatic tools": [[8, "interface-with-other-bioinformatic-tools"]], "Create an interactive analysis report": [[8, "create-an-interactive-analysis-report"]], "What is RNAlysis?": [[9, "what-is-rnalysis"]], "What can I do with RNAlysis?": [[9, "what-can-i-do-with-rnalysis"]], "How do I install it?": [[9, "how-do-i-install-it"]], "How do I use it?": [[9, "how-do-i-use-it"]], "Dependencies": [[9, "dependencies"]], "Credits": [[9, "credits"]], "How do I cite RNAlysis?": [[9, "how-do-i-cite-rnalysis"]], "Development Lead": [[9, "development-lead"]], "Contributors": [[9, "contributors"]], "rnalysis package": [[10, "rnalysis-package"]], "rnalysis.enrichment": [[11, "rnalysis-enrichment"]], "rnalysis.enrichment.FeatureSet": [[12, "rnalysis-enrichment-featureset"]], "rnalysis.enrichment.FeatureSet.add": [[13, "rnalysis-enrichment-featureset-add"]], "rnalysis.enrichment.FeatureSet.biotypes_from_gtf": [[14, "rnalysis-enrichment-featureset-biotypes-from-gtf"]], "rnalysis.enrichment.FeatureSet.biotypes_from_ref_table": [[15, "rnalysis-enrichment-featureset-biotypes-from-ref-table"]], "rnalysis.enrichment.FeatureSet.change_set_name": [[16, "rnalysis-enrichment-featureset-change-set-name"]], "rnalysis.enrichment.FeatureSet.clear": [[17, "rnalysis-enrichment-featureset-clear"]], "rnalysis.enrichment.FeatureSet.copy": [[18, "rnalysis-enrichment-featureset-copy"]], "rnalysis.enrichment.FeatureSet.difference": [[19, "rnalysis-enrichment-featureset-difference"]], "rnalysis.enrichment.FeatureSet.difference_update": [[20, "rnalysis-enrichment-featureset-difference-update"]], "rnalysis.enrichment.FeatureSet.discard": [[21, "rnalysis-enrichment-featureset-discard"]], "rnalysis.enrichment.FeatureSet.filter_biotype_from_gtf": [[22, "rnalysis-enrichment-featureset-filter-biotype-from-gtf"]], "rnalysis.enrichment.FeatureSet.filter_biotype_from_ref_table": [[23, "rnalysis-enrichment-featureset-filter-biotype-from-ref-table"]], "rnalysis.enrichment.FeatureSet.filter_by_attribute": [[24, "rnalysis-enrichment-featureset-filter-by-attribute"]], "rnalysis.enrichment.FeatureSet.filter_by_go_annotations": [[25, "rnalysis-enrichment-featureset-filter-by-go-annotations"]], "rnalysis.enrichment.FeatureSet.filter_by_kegg_annotations": [[26, "rnalysis-enrichment-featureset-filter-by-kegg-annotations"]], "rnalysis.enrichment.FeatureSet.find_paralogs_ensembl": [[27, "rnalysis-enrichment-featureset-find-paralogs-ensembl"]], "rnalysis.enrichment.FeatureSet.find_paralogs_panther": [[28, 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"rnalysis-filtering-foldchangefilter-split-fold-change-direction"]], "rnalysis.filtering.FoldChangeFilter.symmetric_difference": [[327, "rnalysis-filtering-foldchangefilter-symmetric-difference"]], "rnalysis.filtering.FoldChangeFilter.tail": [[328, "rnalysis-filtering-foldchangefilter-tail"]], "rnalysis.filtering.FoldChangeFilter.text_filters": [[329, "rnalysis-filtering-foldchangefilter-text-filters"]], "rnalysis.filtering.FoldChangeFilter.transform": [[330, "rnalysis-filtering-foldchangefilter-transform"]], "rnalysis.filtering.FoldChangeFilter.translate_gene_ids": [[331, "rnalysis-filtering-foldchangefilter-translate-gene-ids"]], "rnalysis.filtering.FoldChangeFilter.union": [[332, "rnalysis-filtering-foldchangefilter-union"]], "rnalysis.filtering.Pipeline": [[333, "rnalysis-filtering-pipeline"]], "rnalysis.filtering.Pipeline.add_function": [[334, "rnalysis-filtering-pipeline-add-function"]], "rnalysis.filtering.Pipeline.apply_to": [[335, "rnalysis-filtering-pipeline-apply-to"]], "rnalysis.filtering.Pipeline.export_pipeline": [[336, "rnalysis-filtering-pipeline-export-pipeline"]], "rnalysis.filtering.Pipeline.import_pipeline": [[337, "rnalysis-filtering-pipeline-import-pipeline"]], "rnalysis.filtering.Pipeline.remove_last_function": [[338, "rnalysis-filtering-pipeline-remove-last-function"]], "rnalysis.general": [[339, "rnalysis-general"]], "rnalysis.general.clear_all_cache": [[340, "rnalysis-general-clear-all-cache"]], "rnalysis.general.clear_gui_cache": [[341, "rnalysis-general-clear-gui-cache"]], "rnalysis.general.parse_gene_name_string": [[342, "rnalysis-general-parse-gene-name-string"]], "rnalysis.general.parse_sequence_name_string": [[343, "rnalysis-general-parse-sequence-name-string"]], "rnalysis.general.parse_wbgene_string": [[344, "rnalysis-general-parse-wbgene-string"]], "rnalysis.general.print_settings_file": [[345, "rnalysis-general-print-settings-file"]], "rnalysis.general.reset_settings_file": [[346, "rnalysis-general-reset-settings-file"]], "rnalysis.general.save_to_csv": [[347, "rnalysis-general-save-to-csv"]], "rnalysis.general.set_attr_ref_table_path": [[348, "rnalysis-general-set-attr-ref-table-path"]], "rnalysis.general.set_biotype_ref_table_path": [[349, "rnalysis-general-set-biotype-ref-table-path"]], "A-to-Z tutorial - example analysis": [[350, "a-to-z-tutorial-example-analysis"]], "Intro and recommendations": [[350, "intro-and-recommendations"]], "Analysis #1 - time series RNA sequencing": [[350, "analysis-1-time-series-rna-sequencing"]], "The dataset": [[350, "the-dataset"], [350, "id6"]], "Start RNAlysis": [[350, "start-rnalysis"]], "Data preprocessing and exploratory data analysis": [[350, "data-preprocessing-and-exploratory-data-analysis"]], "Filter out lowly-expressed genes": [[350, "filter-out-lowly-expressed-genes"]], "Examine variance in our data with Principal Component Analysis": [[350, "examine-variance-in-our-data-with-principal-component-analysis"]], "Examine similarity between developmental stages": [[350, "examine-similarity-between-developmental-stages"]], "Compare the expression of specific genes over the developmental stages": [[350, "compare-the-expression-of-specific-genes-over-the-developmental-stages"]], "Clustering analysis": [[350, "clustering-analysis"]], "The simple approach - distance-based clustering with K-Medoids": [[350, "the-simple-approach-distance-based-clustering-with-k-medoids"]], "Fine-tuning our approach - density-based clustering with HDBSCAN": [[350, "fine-tuning-our-approach-density-based-clustering-with-hdbscan"]], "The complex approach - ensemble-based clustering with CLICOM": [[350, "the-complex-approach-ensemble-based-clustering-with-clicom"]], "Enrichment analysis": [[350, "enrichment-analysis"], [350, "id9"], [352, "enrichment-analysis"]], "Running enrichment analysis": [[350, "running-enrichment-analysis"], [350, "id11"]], "Create analysis report": [[350, "create-analysis-report"]], "Analysis #2 - differential expression data": [[350, "analysis-2-differential-expression-data"]], "Quantify FASTQ files and Differential Expression Analysis": [[350, "quantify-fastq-files-and-differential-expression-analysis"]], "Quality control with FastQC": [[350, "quality-control-with-fastqc"]], "Trim adapters and remove low-quality reads with CutAdapt": [[350, "trim-adapters-and-remove-low-quality-reads-with-cutadapt"]], "Quantify gene expression with kallisto": [[350, "quantify-gene-expression-with-kallisto"]], "Run differential expression analysis with DESeq2": [[350, "run-differential-expression-analysis-with-deseq2"]], "Data filtering and visualization with customized Pipelines": [[350, "data-filtering-and-visualization-with-customized-pipelines"]], "Create a customized Pipeline": [[350, "create-a-customized-pipeline"]], "Apply the Pipeline to our datasets": [[350, "apply-the-pipeline-to-our-datasets"]], "Visualizing and extracting gene set interesctions": [[350, "visualizing-and-extracting-gene-set-interesctions"]], "Create a Venn diagram": [[350, "create-a-venn-diagram"]], "Extract the gene subsets we are interested in": [[350, "extract-the-gene-subsets-we-are-interested-in"]], "Define a background set": [[350, "define-a-background-set"]], "Define our custom enrichment attributes": [[350, "define-our-custom-enrichment-attributes"]], "Final words": [[350, "final-words"]], "User guide - programmatic interface": [[351, "user-guide-programmatic-interface"]], "RNAlysis fastq module": [[351, "rnalysis-fastq-module"]], "Working with the fastq module": [[351, "working-with-the-fastq-module"]], "Adapter trimming with CutAdapt": [[351, "adapter-trimming-with-cutadapt"]], "Single-end adapter trimming": [[351, "single-end-adapter-trimming"]], "Paired-end adapter trimming": [[351, "paired-end-adapter-trimming"]], "RNA sequencing quantification with kallisto": [[351, "rna-sequencing-quantification-with-kallisto"]], "Building or acquiring index files": [[351, "building-or-acquiring-index-files"], [351, "id2"]], "Single-end read quantification": [[351, "single-end-read-quantification"]], "Paired-end read quantification": [[351, "paired-end-read-quantification"]], "Read alignment with bowtie2": [[351, "read-alignment-with-bowtie2"]], "Single-end read alignment": [[351, "single-end-read-alignment"]], "Paired-end read alignment": [[351, "paired-end-read-alignment"]], "Feature counting with featureCounts": [[351, "feature-counting-with-featurecounts"]], "Single-end read feature counting": [[351, "single-end-read-feature-counting"]], "Paired-end read feature counting": [[351, "paired-end-read-feature-counting"]], "RNAlysis filtering module": [[351, "rnalysis-filtering-module"]], "Working with Filter objects": [[351, "working-with-filter-objects"]], "Initialize a Filter object": [[351, "initialize-a-filter-object"]], "View a Filter object": [[351, "view-a-filter-object"]], "Filtering operations": [[351, "filtering-operations"], [352, "filtering-operations"]], "Performing set operations on multiple Filter objects": [[351, "performing-set-operations-on-multiple-filter-objects"]], "Saving Filter results": [[351, "saving-filter-results"]], "Using an Attribute Reference Table for filter operations": [[351, "using-an-attribute-reference-table-for-filter-operations"]], "Using a Biotype Reference Table for filter operations": [[351, "using-a-biotype-reference-table-for-filter-operations"]], "Filtering DESeq2 output files with filtering.DESeqFilter": [[351, "filtering-deseq2-output-files-with-filtering-deseqfilter"]], "Loading from a csv file": [[351, "loading-from-a-csv-file"]], "Filtering operations unique to DESeqFilter": [[351, "filtering-operations-unique-to-deseqfilter"]], "Data visualization and exploratory data analysis with DESeqFilter": [[351, "data-visualization-and-exploratory-data-analysis-with-deseqfilter"]], "Filtering count matrices with filtering.CountFilter": [[351, "filtering-count-matrices-with-filtering-countfilter"]], "Generating an CountFilter object from a folder of HTSeq-count output .txt files": [[351, "generating-an-countfilter-object-from-a-folder-of-htseq-count-output-txt-files"]], "Loading from a pre-made csv file": [[351, "loading-from-a-pre-made-csv-file"]], "Filtering operations unique to CountFilter": [[351, "filtering-operations-unique-to-countfilter"]], "Normalizing reads with CountFilter": [[351, "normalizing-reads-with-countfilter"]], "Data clustering with CountFilter": [[351, "data-clustering-with-countfilter"]], "K-Means clustering": [[351, "k-means-clustering"], [352, "k-means-clustering"]], "K-Medoids clustering": [[351, "k-medoids-clustering"], [352, "k-medoids-clustering"]], "Hierarchical clustering": [[351, "hierarchical-clustering"], [352, "hierarchical-clustering"]], "HDBSCAN clustering": [[351, "hdbscan-clustering"], [352, "hdbscan-clustering"]], "CLICOM clustering": [[351, "clicom-clustering"], [352, "clicom-clustering"]], "Specialized clustering distance metrics": [[351, "specialized-clustering-distance-metrics"], [352, "specialized-clustering-distance-metrics"]], "Data visualization and exploratory data analysis with CountFilter": [[351, "data-visualization-and-exploratory-data-analysis-with-countfilter"]], "Filtering fold-change data of features using filtering.FoldChangeFilter": [[351, "filtering-fold-change-data-of-features-using-filtering-foldchangefilter"]], "Loading fold change data from a csv file": [[351, "loading-fold-change-data-from-a-csv-file"]], "Generating fold change data from an existing CountFilter object": [[351, "generating-fold-change-data-from-an-existing-countfilter-object"]], "Performing randomization tests on a FoldChangeFilter object": [[351, "performing-randomization-tests-on-a-foldchangefilter-object"]], "Sequentially applying filtering operations using Pipelines": [[351, "sequentially-applying-filtering-operations-using-pipelines"]], "Creating a new Pipeline": [[351, "creating-a-new-pipeline"], [352, "creating-a-new-pipeline"]], "Applying Pipelines to Filter objects": [[351, "applying-pipelines-to-filter-objects"]], "Importing a Pipeline": [[351, "importing-a-pipeline"], [352, "importing-a-pipeline"]], "RNAlysis enrichment module": [[351, "rnalysis-enrichment-module"]], "Working with FeatureSet objects": [[351, "working-with-featureset-objects"]], "Initialize an FeatureSet object": [[351, "initialize-an-featureset-object"]], "GO Enrichment": [[351, "go-enrichment"], [352, "go-enrichment"]], "Define the correct organism and gene ID type for your dataset": [[351, "define-the-correct-organism-and-gene-id-type-for-your-dataset"], [351, "id21"], [352, "define-the-correct-organism-and-gene-id-type-for-your-dataset"], [352, "id18"]], "Define the background set": [[351, "define-the-background-set"], [351, "id22"], [351, "id30"], [351, "id38"]], "Choose the statistical test (optional)": [[351, "choose-the-statistical-test-optional"], [351, "id23"], [351, "id31"], [351, "id39"], [352, "choose-the-statistical-test-optional"], [352, "id19"], [352, "id26"], [352, "id33"]], "Filter GO Terms by GO aspects (optional)": [[351, "filter-go-terms-by-go-aspects-optional"], [352, "filter-go-terms-by-go-aspects-optional"]], "Filter GO Annotations by Evidence Codes (optional)": [[351, "filter-go-annotations-by-evidence-codes-optional"], [352, "filter-go-annotations-by-evidence-codes-optional"]], "Filter GO Annotations by database (optional)": [[351, "filter-go-annotations-by-database-optional"], [352, "filter-go-annotations-by-database-optional"]], "Filter GO Annotations by Qualifiers (optional)": [[351, "filter-go-annotations-by-qualifiers-optional"], [352, "filter-go-annotations-by-qualifiers-optional"]], "Choose annotation propagation method (optional)": [[351, "choose-annotation-propagation-method-optional"], [352, "choose-annotation-propagation-method-optional"]], "Choose plotting parameters (optional)": [[351, "choose-plotting-parameters-optional"], [351, "id24"], [351, "id32"], [351, "id40"], [352, "choose-plotting-parameters-optional"], [352, "id20"], [352, "id27"], [352, "id34"]], "Enrichment analysis output": [[351, "enrichment-analysis-output"], [351, "id29"], [351, "id37"], [352, "enrichment-analysis-output"], [352, "id25"], [352, "id32"]], "KEGG Pathways enrichment": [[351, "kegg-pathways-enrichment"], [352, "kegg-pathways-enrichment"]], "Enrichment analysis for user-defined attributes": [[351, "enrichment-analysis-for-user-defined-attributes"], [352, "enrichment-analysis-for-user-defined-attributes"]], "Choose which user-defined attributes to calculate enrichment for": [[351, "choose-which-user-defined-attributes-to-calculate-enrichment-for"], [352, "choose-which-user-defined-attributes-to-calculate-enrichment-for"]], "Performing enrichment analysis for non-categorical user-defined attributes": [[351, "performing-enrichment-analysis-for-non-categorical-user-defined-attributes"], [352, "performing-enrichment-analysis-for-non-categorical-user-defined-attributes"]], "Choose which user-defined non-categorical attributes to calculate enrichment for": [[351, "choose-which-user-defined-non-categorical-attributes-to-calculate-enrichment-for"], [352, "choose-which-user-defined-non-categorical-attributes-to-calculate-enrichment-for"]], "Non-Categorical Enrichment analysis output": [[351, "non-categorical-enrichment-analysis-output"], [352, "non-categorical-enrichment-analysis-output"]], "Performing set operations and visualisation on multiple FeatureSet objects": [[351, "performing-set-operations-and-visualisation-on-multiple-featureset-objects"]], "Saving indices from FeatureSet to a .txt file": [[351, "saving-indices-from-featureset-to-a-txt-file"]], "Working with RankedSet objects": [[351, "working-with-rankedset-objects"]], "Initialize an RankedSet object": [[351, "initialize-an-rankedset-object"]], "Performing single-set GO Enrichment analysis without a background set": [[351, "performing-single-set-go-enrichment-analysis-without-a-background-set"]], "Performing single-set KEGG Enrichment analysis without a background set": [[351, "performing-single-set-kegg-enrichment-analysis-without-a-background-set"]], "Performing single-set enrichment analysis for user-defined attributes without a background set": [[351, "performing-single-set-enrichment-analysis-for-user-defined-attributes-without-a-background-set"]], "Visualizing sets, intersections, and enrichment": [[351, "visualizing-sets-intersections-and-enrichment"]], "Plotting results of enrichment analysis": [[351, "plotting-results-of-enrichment-analysis"]], "Plotting Venn Diagrams and UpSet Plots": [[351, "plotting-venn-diagrams-and-upset-plots"]], "RNAlysis general module": [[351, "rnalysis-general-module"]], "Set and load a Reference Table": [[351, "set-and-load-a-reference-table"], [352, "set-and-load-a-reference-table"]], "What is an Attribute Reference Table?": [[351, "what-is-an-attribute-reference-table"], [352, "what-is-an-attribute-reference-table"]], "What is a Biotype 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your analysis report": [[352, "viewing-your-analysis-report"]], "Open an analysis report": [[352, "open-an-analysis-report"]], "Interacting with the analysis report": [[352, "interacting-with-the-analysis-report"]], "Access the session output files": [[352, "access-the-session-output-files"]], "Sharing your analysis report": [[352, "sharing-your-analysis-report"]], "RNAlysis settings": [[352, "rnalysis-settings"]]}, "indexentries": {"attribute reference table": [[4, "term-Attribute-Reference-Table"]], "biotype reference table": [[4, "term-Biotype-Reference-Table"]], "countfilter": [[4, "term-CountFilter"]], "deseqfilter": [[4, "term-DESeqFilter"]], "featureset": [[4, "term-FeatureSet"]], "filter": [[4, "term-Filter"]], "filter object": [[4, "term-Filter-object"]], "filter objects": [[4, "term-Filter-objects"]], "foldchangefilter": [[4, "term-FoldChangeFilter"]], "pipeline": [[4, "term-Pipeline"]], "rankedset": [[4, "term-RankedSet"]], "module": [[11, "module-rnalysis.enrichment"], [96, "module-rnalysis.fastq"], [129, "module-rnalysis.filtering"], [339, "module-rnalysis.general"]], "rnalysis.enrichment": [[11, "module-rnalysis.enrichment"]], "featureset (class in rnalysis.enrichment)": [[12, "rnalysis.enrichment.FeatureSet"]], "__init__() (rnalysis.enrichment.featureset method)": [[12, "rnalysis.enrichment.FeatureSet.__init__"]], "add() (rnalysis.enrichment.featureset method)": [[13, "rnalysis.enrichment.FeatureSet.add"]], "biotypes_from_gtf() (rnalysis.enrichment.featureset method)": [[14, "rnalysis.enrichment.FeatureSet.biotypes_from_gtf"]], "biotypes_from_ref_table() (rnalysis.enrichment.featureset method)": [[15, "rnalysis.enrichment.FeatureSet.biotypes_from_ref_table"]], "change_set_name() (rnalysis.enrichment.featureset method)": [[16, "rnalysis.enrichment.FeatureSet.change_set_name"]], "clear() (rnalysis.enrichment.featureset method)": [[17, "rnalysis.enrichment.FeatureSet.clear"]], "copy() (rnalysis.enrichment.featureset method)": [[18, 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"rnalysis.enrichment.FeatureSet.filter_by_kegg_annotations"]], "find_paralogs_ensembl() (rnalysis.enrichment.featureset method)": [[27, "rnalysis.enrichment.FeatureSet.find_paralogs_ensembl"]], "find_paralogs_panther() (rnalysis.enrichment.featureset method)": [[28, "rnalysis.enrichment.FeatureSet.find_paralogs_panther"]], "go_enrichment() (rnalysis.enrichment.featureset method)": [[29, "rnalysis.enrichment.FeatureSet.go_enrichment"]], "intersection() (rnalysis.enrichment.featureset method)": [[30, "rnalysis.enrichment.FeatureSet.intersection"]], "intersection_update() (rnalysis.enrichment.featureset method)": [[31, "rnalysis.enrichment.FeatureSet.intersection_update"]], "isdisjoint() (rnalysis.enrichment.featureset method)": [[32, "rnalysis.enrichment.FeatureSet.isdisjoint"]], "issubset() (rnalysis.enrichment.featureset method)": [[33, "rnalysis.enrichment.FeatureSet.issubset"]], "issuperset() (rnalysis.enrichment.featureset method)": [[34, "rnalysis.enrichment.FeatureSet.issuperset"]], "kegg_enrichment() (rnalysis.enrichment.featureset method)": [[35, "rnalysis.enrichment.FeatureSet.kegg_enrichment"]], "map_orthologs_ensembl() (rnalysis.enrichment.featureset method)": [[36, "rnalysis.enrichment.FeatureSet.map_orthologs_ensembl"]], "map_orthologs_orthoinspector() (rnalysis.enrichment.featureset method)": [[37, "rnalysis.enrichment.FeatureSet.map_orthologs_orthoinspector"]], "map_orthologs_panther() (rnalysis.enrichment.featureset method)": [[38, "rnalysis.enrichment.FeatureSet.map_orthologs_panther"]], "map_orthologs_phylomedb() (rnalysis.enrichment.featureset method)": [[39, "rnalysis.enrichment.FeatureSet.map_orthologs_phylomedb"]], "non_categorical_enrichment() (rnalysis.enrichment.featureset method)": [[40, "rnalysis.enrichment.FeatureSet.non_categorical_enrichment"]], "pop() (rnalysis.enrichment.featureset method)": [[41, "rnalysis.enrichment.FeatureSet.pop"]], "remove() (rnalysis.enrichment.featureset method)": 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"rnalysis.enrichment.RankedSet.find_paralogs_panther"]], "go_enrichment() (rnalysis.enrichment.rankedset method)": [[67, "rnalysis.enrichment.RankedSet.go_enrichment"]], "intersection() (rnalysis.enrichment.rankedset method)": [[68, "rnalysis.enrichment.RankedSet.intersection"]], "intersection_update() (rnalysis.enrichment.rankedset method)": [[69, "rnalysis.enrichment.RankedSet.intersection_update"]], "isdisjoint() (rnalysis.enrichment.rankedset method)": [[70, "rnalysis.enrichment.RankedSet.isdisjoint"]], "issubset() (rnalysis.enrichment.rankedset method)": [[71, "rnalysis.enrichment.RankedSet.issubset"]], "issuperset() (rnalysis.enrichment.rankedset method)": [[72, "rnalysis.enrichment.RankedSet.issuperset"]], "kegg_enrichment() (rnalysis.enrichment.rankedset method)": [[73, "rnalysis.enrichment.RankedSet.kegg_enrichment"]], "map_orthologs_ensembl() (rnalysis.enrichment.rankedset method)": [[74, "rnalysis.enrichment.RankedSet.map_orthologs_ensembl"]], "map_orthologs_orthoinspector() (rnalysis.enrichment.rankedset method)": [[75, "rnalysis.enrichment.RankedSet.map_orthologs_orthoinspector"]], "map_orthologs_panther() (rnalysis.enrichment.rankedset method)": [[76, "rnalysis.enrichment.RankedSet.map_orthologs_panther"]], "map_orthologs_phylomedb() (rnalysis.enrichment.rankedset method)": [[77, "rnalysis.enrichment.RankedSet.map_orthologs_phylomedb"]], "non_categorical_enrichment() (rnalysis.enrichment.rankedset method)": [[78, "rnalysis.enrichment.RankedSet.non_categorical_enrichment"]], "pop() (rnalysis.enrichment.rankedset method)": [[79, "rnalysis.enrichment.RankedSet.pop"]], "remove() (rnalysis.enrichment.rankedset method)": [[80, "rnalysis.enrichment.RankedSet.remove"]], "save_txt() (rnalysis.enrichment.rankedset method)": [[81, "rnalysis.enrichment.RankedSet.save_txt"]], "single_set_enrichment() (rnalysis.enrichment.rankedset method)": [[82, "rnalysis.enrichment.RankedSet.single_set_enrichment"]], "single_set_go_enrichment() (rnalysis.enrichment.rankedset method)": [[83, "rnalysis.enrichment.RankedSet.single_set_go_enrichment"]], "single_set_kegg_enrichment() (rnalysis.enrichment.rankedset method)": [[84, "rnalysis.enrichment.RankedSet.single_set_kegg_enrichment"]], "symmetric_difference() (rnalysis.enrichment.rankedset method)": [[85, "rnalysis.enrichment.RankedSet.symmetric_difference"]], "symmetric_difference_update() (rnalysis.enrichment.rankedset method)": [[86, "rnalysis.enrichment.RankedSet.symmetric_difference_update"]], "translate_gene_ids() (rnalysis.enrichment.rankedset method)": [[87, "rnalysis.enrichment.RankedSet.translate_gene_ids"]], "union() (rnalysis.enrichment.rankedset method)": [[88, "rnalysis.enrichment.RankedSet.union"]], "update() (rnalysis.enrichment.rankedset method)": [[89, "rnalysis.enrichment.RankedSet.update"]], "user_defined_enrichment() (rnalysis.enrichment.rankedset method)": [[90, "rnalysis.enrichment.RankedSet.user_defined_enrichment"]], "enrichment_bar_plot() (in module rnalysis.enrichment)": [[91, "rnalysis.enrichment.enrichment_bar_plot"]], "gene_ontology_graph() (in module rnalysis.enrichment)": [[92, "rnalysis.enrichment.gene_ontology_graph"]], "kegg_pathway_graph() (in module rnalysis.enrichment)": [[93, "rnalysis.enrichment.kegg_pathway_graph"]], "upset_plot() (in module rnalysis.enrichment)": [[94, "rnalysis.enrichment.upset_plot"]], "venn_diagram() (in module rnalysis.enrichment)": [[95, "rnalysis.enrichment.venn_diagram"]], "rnalysis.fastq": [[96, "module-rnalysis.fastq"]], "pairedendpipeline (class in rnalysis.fastq)": [[97, "rnalysis.fastq.PairedEndPipeline"]], "__init__() (rnalysis.fastq.pairedendpipeline method)": [[97, "rnalysis.fastq.PairedEndPipeline.__init__"]], "add_function() (rnalysis.fastq.pairedendpipeline method)": [[98, "rnalysis.fastq.PairedEndPipeline.add_function"]], "apply_to() (rnalysis.fastq.pairedendpipeline method)": [[99, "rnalysis.fastq.PairedEndPipeline.apply_to"]], "export_pipeline() (rnalysis.fastq.pairedendpipeline method)": [[100, "rnalysis.fastq.PairedEndPipeline.export_pipeline"]], "import_pipeline() (rnalysis.fastq.pairedendpipeline class method)": [[101, "rnalysis.fastq.PairedEndPipeline.import_pipeline"]], "remove_last_function() (rnalysis.fastq.pairedendpipeline method)": [[102, "rnalysis.fastq.PairedEndPipeline.remove_last_function"]], "singleendpipeline (class in rnalysis.fastq)": [[103, "rnalysis.fastq.SingleEndPipeline"]], "__init__() (rnalysis.fastq.singleendpipeline method)": [[103, "rnalysis.fastq.SingleEndPipeline.__init__"]], "add_function() (rnalysis.fastq.singleendpipeline method)": [[104, "rnalysis.fastq.SingleEndPipeline.add_function"]], "apply_to() (rnalysis.fastq.singleendpipeline method)": [[105, "rnalysis.fastq.SingleEndPipeline.apply_to"]], "export_pipeline() (rnalysis.fastq.singleendpipeline method)": [[106, "rnalysis.fastq.SingleEndPipeline.export_pipeline"]], "import_pipeline() (rnalysis.fastq.singleendpipeline class method)": [[107, 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49, 67, 73, 82, 83, 84, 90, 192, 193, 194, 195, 196, 289, 350, 351, 352], "unexpect": 0, "result": [0, 5, 8, 10, 11, 29, 35, 40, 49, 67, 73, 78, 82, 83, 84, 90, 91, 92, 109, 110, 116, 117, 120, 121, 138, 139, 151, 188, 189, 191, 192, 193, 194, 195, 196, 200, 219, 239, 240, 241, 245, 262, 281, 282, 286, 319, 324, 326, 335, 339, 350, 352], "The": [0, 1, 2, 4, 5, 7, 8, 9, 10, 14, 19, 22, 23, 29, 30, 35, 40, 47, 49, 52, 57, 60, 61, 67, 68, 73, 78, 82, 83, 84, 88, 90, 92, 93, 96, 109, 110, 111, 116, 117, 118, 119, 120, 121, 124, 125, 126, 127, 130, 132, 133, 134, 135, 136, 138, 139, 140, 141, 142, 143, 148, 150, 152, 158, 159, 162, 163, 172, 175, 178, 179, 180, 189, 191, 192, 193, 194, 195, 196, 200, 203, 204, 205, 206, 207, 209, 210, 211, 212, 220, 228, 240, 241, 245, 248, 249, 250, 251, 252, 254, 255, 256, 263, 270, 282, 286, 289, 290, 291, 292, 294, 295, 296, 297, 305, 312, 319, 325, 326, 330, 333, 342, 343, 344, 351, 352], "provid": [0, 1, 5, 7, 10, 14, 52, 96, 124, 132, 133, 193, 205, 206, 221, 250, 251, 290, 291, 350, 351, 352], "unifi": [0, 96, 351], "programmat": [0, 1, 5, 6, 7, 9, 96, 350], "interfac": [0, 1, 5, 6, 7, 9, 96, 350], "extern": [0, 5, 7, 96, 351], "tool": [0, 5, 6, 9, 96, 120, 121, 350, 351, 352], "process": [0, 2, 5, 7, 10, 29, 35, 49, 67, 73, 82, 83, 84, 90, 96, 118, 126, 127, 192, 193, 194, 195, 196, 350, 351, 352], "file": [0, 1, 4, 5, 7, 8, 10, 11, 14, 15, 22, 23, 29, 35, 40, 43, 49, 52, 53, 60, 61, 67, 73, 78, 81, 82, 83, 84, 90, 92, 93, 96, 100, 101, 106, 107, 109, 110, 111, 112, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 132, 138, 139, 142, 143, 158, 159, 172, 174, 175, 176, 182, 183, 184, 204, 205, 211, 212, 235, 236, 237, 249, 250, 255, 256, 277, 278, 279, 289, 290, 296, 297, 319, 320, 321, 322, 336, 337, 339, 345, 346, 347, 348, 349], "those": [0, 2, 8, 10, 93, 96, 109, 110, 168, 171, 192, 193, 194, 195, 196, 339, 350, 351, 352], "current": [0, 1, 2, 5, 10, 19, 22, 23, 24, 25, 26, 30, 36, 37, 38, 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126, 127], "trim": [0, 5, 7, 8, 9, 10, 96, 122, 123, 124, 126, 127, 170, 352], "kallisto": [0, 5, 7, 9, 96, 119, 120, 121], "rna": [0, 5, 6, 7, 9, 10, 96, 124, 130, 174, 352], "sequenc": [0, 5, 6, 9, 10, 93, 96, 109, 110, 111, 116, 117, 118, 119, 120, 121, 124, 126, 127, 128, 185, 342, 343, 352], "quantif": [0, 5, 7, 9, 96, 120, 121, 350], "bowtie2": [0, 5, 9, 96, 109, 110, 111, 116, 117], "align": [0, 5, 8, 9, 10, 96, 109, 110, 111, 116, 117, 122, 123, 124, 125, 158, 159, 174, 194, 350, 352], "featurecount": [0, 5, 96, 116, 117], "featur": [0, 4, 5, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 43, 46, 49, 50, 52, 60, 61, 62, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 78, 81, 83, 84, 87, 90, 93, 94, 95, 96, 116, 117, 120, 121, 130, 132, 133, 137, 142, 143, 144, 145, 146, 148, 150, 151, 152, 153, 154, 155, 159, 161, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 180, 181, 185, 188, 189, 191, 192, 193, 194, 195, 196, 197, 199, 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342, 343, 344, 346, 350], "list": [0, 1, 4, 5, 6, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 43, 49, 50, 60, 61, 62, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 78, 81, 82, 83, 84, 90, 95, 99, 109, 110, 111, 112, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 130, 131, 134, 135, 136, 140, 141, 142, 143, 144, 145, 146, 147, 153, 154, 155, 156, 162, 164, 165, 166, 167, 168, 178, 179, 180, 185, 186, 187, 188, 190, 192, 193, 194, 195, 196, 200, 203, 204, 207, 209, 211, 212, 213, 214, 215, 216, 222, 223, 224, 229, 230, 231, 232, 238, 239, 245, 249, 252, 254, 255, 256, 257, 258, 259, 260, 264, 265, 266, 271, 272, 273, 274, 280, 281, 286, 289, 292, 294, 296, 297, 298, 299, 300, 301, 306, 307, 308, 313, 314, 315, 316, 323, 324, 333, 350, 351, 352], "perform": [0, 2, 4, 5, 6, 9, 10, 11, 25, 29, 40, 63, 67, 78, 83, 124, 129, 135, 145, 152, 179, 186, 187, 189, 190, 214, 220, 238, 240, 258, 263, 280, 282, 299, 319, 323, 350], "classmethod": [0, 10, 101, 107, 157, 158, 159, 225, 267, 309, 337], "import_pipelin": [0, 10, 351], "genericpipelin": [0, 10, 101, 107, 337], "import": [0, 5, 6, 7, 9, 10, 12, 15, 19, 30, 44, 47, 50, 53, 57, 68, 85, 88, 101, 102, 107, 108, 129, 133, 136, 137, 143, 144, 148, 150, 151, 152, 153, 156, 158, 159, 160, 161, 163, 168, 169, 170, 171, 173, 174, 176, 177, 181, 186, 188, 189, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 202, 206, 207, 208, 210, 212, 213, 218, 219, 220, 221, 222, 226, 227, 228, 233, 234, 238, 239, 240, 241, 242, 243, 244, 245, 247, 249, 251, 252, 253, 256, 257, 262, 263, 264, 268, 269, 270, 275, 276, 280, 281, 282, 283, 284, 285, 286, 288, 289, 291, 292, 293, 295, 297, 298, 303, 306, 310, 311, 312, 317, 318, 319, 323, 324, 326, 327, 328, 329, 332, 333, 334, 335, 337, 338, 342, 343, 344, 345, 348, 349], "from": [0, 1, 2, 4, 5, 6, 8, 9, 10, 12, 14, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 42, 44, 46, 47, 49, 50, 52, 53, 55, 57, 58, 59, 60, 61, 62, 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302, 303, 306, 307, 308, 309, 313, 314, 315, 316, 317, 319, 320, 321, 322, 323, 324, 326, 329, 330, 331, 334, 337, 342, 343, 347, 350, 352], "contain": [0, 2, 4, 5, 10, 14, 22, 33, 34, 52, 60, 71, 72, 91, 92, 101, 107, 110, 111, 112, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 127, 128, 130, 132, 137, 138, 139, 142, 158, 159, 161, 168, 169, 170, 171, 172, 173, 174, 175, 176, 188, 189, 191, 192, 193, 199, 204, 205, 208, 211, 227, 239, 240, 241, 244, 249, 250, 253, 255, 269, 281, 282, 285, 289, 290, 293, 296, 311, 319, 324, 325, 326, 329, 337, 339, 342, 343, 344, 350, 351, 352], "param": [0, 10, 14, 25, 26, 29, 39, 52, 63, 64, 67, 77, 83, 111, 122, 132, 133, 134, 145, 146, 151, 162, 167, 172, 175, 178, 203, 205, 206, 214, 215, 219, 232, 248, 250, 251, 258, 259, 262, 274, 290, 291, 299, 300, 316, 333, 334, 342, 343, 344, 347, 348, 349], "remove_last_funct": [0, 10, 351], "remov": [0, 9, 10, 17, 20, 21, 36, 37, 38, 39, 41, 55, 58, 59, 74, 75, 76, 77, 79, 102, 108, 118, 130, 147, 148, 149, 150, 151, 152, 164, 165, 166, 167, 204, 216, 217, 219, 220, 221, 229, 230, 231, 232, 249, 260, 261, 262, 263, 271, 272, 273, 274, 289, 301, 302, 304, 305, 313, 314, 315, 316, 338, 351, 352], "last": [0, 5, 10, 36, 37, 38, 39, 74, 75, 76, 77, 102, 108, 149, 153, 164, 165, 166, 167, 186, 198, 217, 222, 229, 230, 231, 232, 238, 243, 261, 264, 271, 272, 273, 274, 280, 284, 302, 306, 313, 314, 315, 316, 323, 328, 338, 350, 351, 352], "wa": [0, 2, 5, 7, 9, 10, 102, 108, 126, 127, 130, 152, 159, 220, 263, 305, 338, 350, 351, 352], "ad": [0, 8, 10, 39, 77, 102, 108, 167, 170, 178, 232, 274, 316, 334, 335, 338, 350, 351, 352], "place": [0, 2, 5, 6, 10, 102, 108, 137, 161, 186, 187, 208, 227, 238, 253, 269, 280, 293, 311, 323, 335, 338, 351, 352], "exampl": [0, 1, 2, 5, 6, 7, 8, 10, 12, 15, 19, 22, 23, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 44, 46, 47, 49, 50, 53, 57, 60, 61, 63, 64, 65, 66, 67, 68, 73, 74, 75, 76, 77, 78, 82, 83, 84, 85, 87, 88, 90, 93, 94, 95, 102, 108, 109, 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349, 351, 352], "pipe": [0, 10, 102, 108, 333, 334, 335, 338, 351], "add_funct": [0, 10, 102, 108, 335, 338, 351], "filter_missing_valu": [0, 5, 10, 102, 108, 334, 335, 338, 351], "singleendpipelin": [0, 5], "abc": 0, "_merge_kallisto_output": 0, "output_fold": [0, 5, 10, 99, 105, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 138, 139, 351], "output": [0, 2, 4, 5, 10, 22, 23, 24, 25, 26, 43, 60, 61, 62, 63, 64, 81, 109, 110, 118, 120, 121, 122, 123, 126, 127, 136, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 174, 177, 195, 196, 199, 204, 207, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 233, 244, 249, 252, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 275, 285, 292, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 317, 329, 335, 350], "merg": [0, 1, 10, 124, 193, 194, 350, 351, 352], "csv": [0, 2, 4, 5, 10, 11, 12, 15, 29, 35, 40, 49, 50, 53, 67, 73, 78, 82, 83, 84, 90, 120, 121, 129, 130, 133, 136, 137, 138, 139, 143, 144, 148, 150, 151, 152, 153, 156, 158, 159, 160, 161, 163, 168, 169, 170, 171, 173, 174, 176, 177, 181, 182, 184, 186, 188, 189, 191, 197, 198, 199, 200, 202, 204, 206, 207, 208, 210, 212, 213, 218, 219, 220, 221, 222, 226, 227, 228, 233, 234, 235, 237, 238, 239, 240, 241, 242, 243, 244, 245, 247, 249, 251, 252, 253, 256, 257, 262, 263, 264, 268, 269, 270, 275, 276, 277, 279, 280, 281, 282, 283, 284, 285, 286, 288, 289, 291, 292, 293, 295, 297, 298, 303, 306, 310, 311, 312, 317, 318, 319, 320, 322, 323, 324, 326, 327, 328, 329, 332, 335, 347, 350], "transcript": [0, 5, 7, 10, 14, 22, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 46, 52, 60, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 87, 93, 116, 117, 120, 121, 132, 142, 145, 146, 154, 155, 164, 165, 166, 167, 172, 175, 201, 205, 211, 214, 215, 223, 224, 229, 230, 231, 232, 246, 250, 255, 258, 259, 265, 266, 271, 272, 273, 274, 287, 290, 296, 299, 300, 307, 308, 313, 314, 315, 316, 331, 350, 351], "estim": [0, 5, 9, 10, 120, 121, 194, 195, 196, 350, 351, 352], "tpm": [0, 5, 10, 120, 121, 150, 175, 185, 191, 350, 351], "bowtie2_align_paired_end": [0, 351], "r1_file": [0, 99, 109, 114, 120, 126, 351], "r2_file": [0, 99, 109, 114, 120, 126, 351], "index_fil": [0, 109, 110, 120, 121, 351], "bowtie2_installation_fold": [0, 109, 110, 111], "liter": [0, 10, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 46, 49, 52, 53, 60, 61, 62, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 78, 82, 83, 84, 87, 90, 91, 92, 93, 94, 95, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 131, 132, 133, 134, 135, 137, 138, 139, 141, 142, 143, 144, 145, 146, 149, 151, 154, 155, 161, 162, 163, 164, 165, 166, 167, 170, 172, 175, 177, 178, 179, 180, 184, 185, 188, 192, 193, 194, 195, 196, 197, 199, 200, 201, 202, 203, 205, 206, 208, 211, 212, 213, 214, 215, 217, 218, 219, 223, 224, 227, 228, 229, 230, 231, 232, 233, 237, 239, 242, 244, 245, 246, 247, 248, 250, 251, 253, 255, 256, 257, 258, 259, 261, 262, 265, 266, 269, 270, 271, 272, 273, 274, 275, 279, 281, 283, 285, 286, 287, 288, 290, 291, 293, 296, 297, 298, 299, 300, 302, 303, 307, 308, 311, 312, 313, 314, 315, 316, 317, 322, 324, 327, 329, 330, 331, 332], "auto": [0, 5, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 46, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 83, 84, 87, 91, 92, 93, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 131, 134, 135, 138, 139, 141, 145, 146, 154, 155, 162, 164, 165, 166, 167, 170, 178, 179, 185, 194, 195, 196, 201, 203, 214, 215, 223, 224, 229, 230, 231, 232, 246, 248, 258, 259, 265, 266, 271, 272, 273, 274, 287, 299, 300, 307, 308, 313, 314, 315, 316, 331, 350, 351, 352], "new_sample_nam": [0, 109, 110, 112, 114, 115, 116, 117, 118, 120, 121, 122, 123, 124, 125, 126, 127, 128, 350], "mode": [0, 2, 5, 10, 24, 25, 26, 62, 63, 64, 109, 110, 124, 144, 145, 146, 185, 213, 214, 215, 248, 257, 258, 259, 298, 299, 300, 351], "end": [0, 5, 10, 109, 110, 116, 117, 120, 121, 122, 123, 124, 126, 127, 153, 186, 199, 222, 238, 244, 264, 280, 285, 306, 323, 329, 350, 352], "local": [0, 1, 2, 10, 109, 110, 346, 350], "settings_preset": [0, 109, 110], "veri": [0, 2, 109, 110, 350, 351, 352], "fast": [0, 9, 109, 110], "sensit": [0, 109, 110, 351, 352], "ignore_qu": [0, 109, 110], "bool": [0, 10, 22, 23, 24, 25, 26, 27, 29, 35, 36, 37, 38, 39, 40, 46, 49, 60, 61, 62, 63, 64, 65, 67, 73, 74, 75, 76, 77, 78, 82, 83, 84, 87, 90, 91, 94, 95, 109, 110, 116, 117, 119, 120, 121, 122, 123, 124, 126, 127, 128, 130, 131, 132, 133, 134, 137, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 157, 158, 159, 161, 162, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 185, 186, 187, 190, 192, 193, 194, 195, 196, 199, 200, 201, 204, 205, 206, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 225, 227, 229, 230, 231, 232, 233, 238, 244, 245, 246, 248, 250, 251, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 269, 271, 272, 273, 274, 275, 280, 285, 286, 287, 289, 290, 291, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 309, 311, 313, 314, 315, 316, 317, 319, 323, 329, 330, 331, 335], "fals": [0, 2, 5, 10, 22, 23, 24, 25, 26, 29, 35, 36, 37, 38, 39, 40, 46, 49, 60, 61, 62, 63, 64, 67, 73, 74, 75, 76, 77, 78, 82, 83, 84, 87, 90, 91, 109, 110, 116, 117, 119, 120, 121, 122, 123, 124, 126, 127, 128, 130, 131, 132, 133, 134, 137, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 157, 158, 159, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 185, 192, 193, 194, 195, 196, 199, 200, 201, 204, 205, 206, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 225, 227, 228, 229, 230, 231, 232, 233, 234, 244, 245, 246, 248, 250, 251, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 269, 270, 271, 272, 273, 274, 275, 276, 285, 286, 287, 289, 290, 291, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 309, 311, 312, 313, 314, 315, 316, 317, 318, 319, 329, 330, 331, 334, 335, 350, 351, 352], "quality_score_typ": [0, 109, 110, 114, 115], "phred33": [0, 109, 110, 114, 115], "phred64": [0, 109, 110, 114, 115], "solexa": [0, 109, 110, 114, 115], "qual": [0, 109, 110, 114, 115], "int": [0, 5, 10, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 49, 63, 64, 65, 66, 67, 73, 74, 75, 76, 77, 78, 82, 83, 84, 90, 91, 92, 93, 109, 110, 111, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 126, 127, 145, 146, 153, 154, 155, 160, 164, 165, 166, 167, 168, 179, 185, 187, 190, 192, 193, 194, 195, 196, 198, 199, 210, 214, 215, 222, 223, 224, 226, 229, 230, 231, 232, 243, 244, 258, 259, 264, 265, 266, 268, 271, 272, 273, 274, 284, 285, 295, 299, 300, 306, 307, 308, 310, 313, 314, 315, 316, 319, 328, 329], "mate_orient": [0, 109], "fwd": [0, 109], "rev": [0, 109, 111], "min_fragment_length": [0, 109, 116], "nonnegativeint": [0, 10, 109, 110, 111, 116, 126, 127, 153, 168, 195, 196, 222, 264, 306], "0": [0, 2, 7, 9, 10, 29, 35, 39, 40, 49, 67, 73, 77, 78, 82, 83, 84, 90, 91, 95, 109, 110, 111, 116, 117, 120, 121, 124, 126, 127, 133, 136, 143, 152, 160, 163, 167, 168, 170, 171, 185, 186, 189, 190, 192, 193, 206, 207, 210, 212, 220, 221, 226, 228, 232, 238, 240, 248, 251, 252, 256, 263, 268, 270, 274, 280, 282, 289, 291, 292, 295, 297, 305, 310, 312, 316, 319, 323, 325, 326, 334, 342, 343, 350, 351, 352], "max_fragment_length": [0, 109, 116], "positiveint": [0, 10, 29, 35, 40, 49, 67, 73, 78, 82, 83, 84, 90, 91, 92, 93, 109, 110, 111, 116, 117, 119, 120, 121, 122, 123, 124, 126, 127, 160, 179, 187, 190, 192, 193, 194, 195, 196, 198, 226, 243, 268, 284, 310, 319, 328], "500": [0, 109, 351], "allow_individual_align": [0, 109], "true": [0, 5, 10, 14, 22, 23, 24, 25, 26, 27, 29, 32, 35, 36, 37, 38, 39, 40, 46, 49, 52, 60, 61, 62, 63, 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29, 35, 49, 67, 73, 82, 83, 84, 90, 109, 110, 111, 116, 117, 124, 192, 193, 194, 195, 196], "1": [0, 2, 6, 9, 10, 15, 29, 35, 39, 40, 49, 53, 67, 73, 77, 78, 82, 83, 84, 90, 91, 95, 109, 110, 111, 116, 117, 119, 120, 124, 126, 127, 133, 134, 135, 136, 138, 139, 141, 151, 152, 160, 163, 167, 168, 170, 171, 178, 185, 186, 189, 190, 192, 193, 198, 200, 203, 206, 207, 210, 219, 220, 221, 226, 228, 232, 238, 240, 243, 245, 248, 251, 252, 262, 263, 268, 270, 274, 280, 282, 284, 286, 291, 292, 295, 305, 310, 312, 316, 319, 323, 325, 328, 330, 334, 342, 351, 352], "pair": [0, 5, 10, 36, 37, 38, 39, 74, 75, 76, 77, 109, 110, 116, 120, 121, 122, 123, 124, 126, 164, 165, 166, 167, 178, 179, 192, 194, 229, 230, 231, 232, 271, 272, 273, 274, 313, 314, 315, 316, 350, 352], "read": [0, 2, 5, 9, 10, 24, 25, 29, 38, 39, 62, 63, 67, 76, 77, 83, 109, 110, 116, 117, 118, 120, 121, 122, 123, 124, 126, 127, 128, 129, 134, 135, 138, 139, 141, 144, 145, 150, 159, 166, 167, 168, 170, 171, 172, 173, 174, 175, 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What should I do?": [[2, "i-am-trying-to-open-rnalysis-for-the-first-time-and-it-takes-a-long-time-to-load-doesn-t-load-at-all-what-should-i-do"]], "Can I install a previous version of RNAlysis?": [[2, "can-i-install-a-previous-version-of-rnalysis"]], "Usage": [[2, "usage"]], "I am trying to view the RNAlysis quick-start guide, but see only blank pages. What should I do?": [[2, "i-am-trying-to-view-the-rnalysis-quick-start-guide-but-see-only-blank-pages-what-should-i-do"]], "I am trying to apply a function to my data table. How do I know what all the different functions and parmeters do?": [[2, "i-am-trying-to-apply-a-function-to-my-data-table-how-do-i-know-what-all-the-different-functions-and-parmeters-do"]], "I want to use a particular statistical method or algorithm available in RNAlysis. How do I know exactly what it does and how it works?": [[2, "i-want-to-use-a-particular-statistical-method-or-algorithm-available-in-rnalysis-how-do-i-know-exactly-what-it-does-and-how-it-works"]], "What file formats are supported by RNAlysis?": [[2, "what-file-formats-are-supported-by-rnalysis"]], "What types of tables can I analyze with RNAlysis?": [[2, "what-types-of-tables-can-i-analyze-with-rnalysis"]], "When trying to run clustering/enrichment/other functions in RNAlysis, a progress bar appears but nothing happens. What can I do?": [[2, "when-trying-to-run-clustering-enrichment-other-functions-in-rnalysis-a-progress-bar-appears-but-nothing-happens-what-can-i-do"]], "I ran into a problem that is not specified here. What can I do?": [[2, "i-ran-into-a-problem-that-is-not-specified-here-what-can-i-do"]], "Automatic analysis reports": [[2, "automatic-analysis-reports"]], "How can I generate an analysis report?": [[2, "how-can-i-generate-an-analysis-report"]], "How can I view an analysis report?": [[2, "how-can-i-view-an-analysis-report"]], "How can I share an analysis report?": [[2, "how-can-i-share-an-analysis-report"]], "How can I access the data and figures that appear in an analysis report?": [[2, "how-can-i-access-the-data-and-figures-that-appear-in-an-analysis-report"]], "Do I need to generate analysis reports manually?": [[2, "do-i-need-to-generate-analysis-reports-manually"]], "Can I edit my analysis report?": [[2, "can-i-edit-my-analysis-report"]], "RNAlysis crashed during an analysis! Can I restore my automatic analysis report?": [[2, "rnalysis-crashed-during-an-analysis-can-i-restore-my-automatic-analysis-report"]], "Can I create an analysis report through the programmatic interface?": [[2, "can-i-create-an-analysis-report-through-the-programmatic-interface"]], "Index": [[3, "index"]], "Glossary - programmatic interface": [[4, "glossary-programmatic-interface"]], "RNAlysis 3.11.0 documentation": [[6, "rnalysis-release-documentation"]], "About RNAlysis:": [[6, null]], "Starting with RNAlysis:": [[6, null]], "Change history:": [[6, null]], "Modules:": [[6, "modules"]], "Indices and tables:": [[6, null]], "RNAlysis stand-alone app (most beginner-friendly)": [[7, "rnalysis-stand-alone-app-most-beginner-friendly"]], "How to install it": [[7, "how-to-install-it"], [7, "id1"], [7, "id3"]], "How to run it": [[7, "how-to-run-it"], [7, "id2"], [7, "id4"]], "Further guidance": [[7, "further-guidance"]], "Install as a Python package with pip (best performance)": [[7, "install-as-a-python-package-with-pip-best-performance"]], "From sources": [[7, "from-sources"]], "RNAlysis quick-start video guide": [[8, "rnalysis-quick-start-video-guide"]], "Open the program": [[8, "open-the-program"]], "Load a table": [[8, "load-a-table"]], "Examine your table": [[8, "examine-your-table"]], "Filter your table": [[8, "filter-your-table"]], "Undo the operations you applied to your table": [[8, "undo-the-operations-you-applied-to-your-table"]], "Apply your operations \u2018in-place\u2019 or apply on a new table": [[8, "apply-your-operations-in-place-or-apply-on-a-new-table"]], "Save the changes you made to your table": [[8, "save-the-changes-you-made-to-your-table"]], "Work on multiple tables at the same time": [[8, "work-on-multiple-tables-at-the-same-time"]], "Different types of tables offer different ways to filter and analyze your data": [[8, "different-types-of-tables-offer-different-ways-to-filter-and-analyze-your-data"]], "Create and save graphs": [[8, "create-and-save-graphs"]], "Quickly look-up genes in your database of choice": [[8, "quickly-look-up-genes-in-your-database-of-choice"]], "Sort your tabs and change their icons": [[8, "sort-your-tabs-and-change-their-icons"]], "Restore tabs you closed": [[8, "restore-tabs-you-closed"]], "Import lists of genes as Gene Sets": [[8, "import-lists-of-genes-as-gene-sets"]], "Visualize the intersections between your tables and gene sets": [[8, "visualize-the-intersections-between-your-tables-and-gene-sets"]], "Apply set operations to your tables and gene sets": [[8, "apply-set-operations-to-your-tables-and-gene-sets"]], "Perform enrichment analysis on your tables and gene sets": [[8, "perform-enrichment-analysis-on-your-tables-and-gene-sets"]], "Create Pipelines to streamline your data analysis": [[8, "create-pipelines-to-streamline-your-data-analysis"]], "Apply Pipelines to one or more of your tables": [[8, "apply-pipelines-to-one-or-more-of-your-tables"]], "Export and share Pipelines to make your analysis more reproducible": [[8, "export-and-share-pipelines-to-make-your-analysis-more-reproducible"]], "Interface with other bioinformatic tools": [[8, "interface-with-other-bioinformatic-tools"]], "Create an interactive analysis report": [[8, "create-an-interactive-analysis-report"]], "What is RNAlysis?": [[9, "what-is-rnalysis"]], "What can I do with RNAlysis?": [[9, "what-can-i-do-with-rnalysis"]], "How do I install it?": [[9, "how-do-i-install-it"]], "How do I use it?": [[9, "how-do-i-use-it"]], "Dependencies": [[9, "dependencies"]], "Credits": [[9, "credits"]], "How do I cite RNAlysis?": [[9, "how-do-i-cite-rnalysis"]], "Development Lead": [[9, "development-lead"]], "Contributors": [[9, "contributors"]], "rnalysis.enrichment": [[11, "rnalysis-enrichment"]], "rnalysis.enrichment.FeatureSet.add": [[13, "rnalysis-enrichment-featureset-add"]], "rnalysis.enrichment.FeatureSet.biotypes_from_ref_table": [[15, "rnalysis-enrichment-featureset-biotypes-from-ref-table"]], "rnalysis.enrichment.FeatureSet.change_set_name": [[16, "rnalysis-enrichment-featureset-change-set-name"]], "rnalysis.enrichment.FeatureSet.clear": [[17, "rnalysis-enrichment-featureset-clear"]], "rnalysis.enrichment.FeatureSet.copy": [[18, "rnalysis-enrichment-featureset-copy"]], "rnalysis.enrichment.FeatureSet.difference": [[19, "rnalysis-enrichment-featureset-difference"]], "rnalysis.enrichment.FeatureSet.difference_update": [[20, "rnalysis-enrichment-featureset-difference-update"]], "rnalysis.enrichment.FeatureSet.discard": [[21, "rnalysis-enrichment-featureset-discard"]], "rnalysis.enrichment.FeatureSet.filter_by_attribute": [[24, "rnalysis-enrichment-featureset-filter-by-attribute"]], "rnalysis.enrichment.FeatureSet.filter_by_go_annotations": [[25, "rnalysis-enrichment-featureset-filter-by-go-annotations"]], "rnalysis.enrichment.FeatureSet.filter_by_kegg_annotations": [[26, "rnalysis-enrichment-featureset-filter-by-kegg-annotations"]], "rnalysis.enrichment.FeatureSet.go_enrichment": [[29, "rnalysis-enrichment-featureset-go-enrichment"]], "rnalysis.enrichment.FeatureSet.intersection": [[30, "rnalysis-enrichment-featureset-intersection"]], "rnalysis.enrichment.FeatureSet.intersection_update": [[31, "rnalysis-enrichment-featureset-intersection-update"]], "rnalysis.enrichment.FeatureSet.isdisjoint": [[32, "rnalysis-enrichment-featureset-isdisjoint"]], "rnalysis.enrichment.FeatureSet.issubset": [[33, "rnalysis-enrichment-featureset-issubset"]], "rnalysis.enrichment.FeatureSet.issuperset": [[34, "rnalysis-enrichment-featureset-issuperset"]], "rnalysis.enrichment.FeatureSet.kegg_enrichment": [[35, "rnalysis-enrichment-featureset-kegg-enrichment"]], "rnalysis.enrichment.FeatureSet.non_categorical_enrichment": [[40, "rnalysis-enrichment-featureset-non-categorical-enrichment"]], "rnalysis.enrichment.FeatureSet.pop": [[41, "rnalysis-enrichment-featureset-pop"]], "rnalysis.enrichment.FeatureSet.remove": [[42, "rnalysis-enrichment-featureset-remove"]], "rnalysis.enrichment.FeatureSet.save_txt": [[43, "rnalysis-enrichment-featureset-save-txt"]], "rnalysis.enrichment.FeatureSet.symmetric_difference": [[44, "rnalysis-enrichment-featureset-symmetric-difference"]], "rnalysis.enrichment.FeatureSet.symmetric_difference_update": [[45, "rnalysis-enrichment-featureset-symmetric-difference-update"]], "rnalysis.enrichment.FeatureSet.translate_gene_ids": [[46, "rnalysis-enrichment-featureset-translate-gene-ids"]], "rnalysis.enrichment.FeatureSet.union": [[47, "rnalysis-enrichment-featureset-union"]], "rnalysis.enrichment.FeatureSet.update": [[48, "rnalysis-enrichment-featureset-update"]], "rnalysis.enrichment.FeatureSet.user_defined_enrichment": [[49, "rnalysis-enrichment-featureset-user-defined-enrichment"]], "rnalysis.enrichment.RankedSet.add": [[51, "rnalysis-enrichment-rankedset-add"]], "rnalysis.enrichment.RankedSet.biotypes_from_ref_table": [[53, "rnalysis-enrichment-rankedset-biotypes-from-ref-table"]], "rnalysis.enrichment.RankedSet.change_set_name": [[54, "rnalysis-enrichment-rankedset-change-set-name"]], "rnalysis.enrichment.RankedSet.clear": [[55, "rnalysis-enrichment-rankedset-clear"]], "rnalysis.enrichment.RankedSet.copy": [[56, "rnalysis-enrichment-rankedset-copy"]], "rnalysis.enrichment.RankedSet.difference": [[57, "rnalysis-enrichment-rankedset-difference"]], "rnalysis.enrichment.RankedSet.difference_update": [[58, "rnalysis-enrichment-rankedset-difference-update"]], "rnalysis.enrichment.RankedSet.discard": [[59, "rnalysis-enrichment-rankedset-discard"]], "rnalysis.enrichment.RankedSet.filter_by_attribute": [[62, "rnalysis-enrichment-rankedset-filter-by-attribute"]], "rnalysis.enrichment.RankedSet.filter_by_go_annotations": [[63, "rnalysis-enrichment-rankedset-filter-by-go-annotations"]], "rnalysis.enrichment.RankedSet.filter_by_kegg_annotations": [[64, "rnalysis-enrichment-rankedset-filter-by-kegg-annotations"]], "rnalysis.enrichment.RankedSet.go_enrichment": [[67, "rnalysis-enrichment-rankedset-go-enrichment"]], "rnalysis.enrichment.RankedSet.intersection": [[68, "rnalysis-enrichment-rankedset-intersection"]], "rnalysis.enrichment.RankedSet.intersection_update": [[69, "rnalysis-enrichment-rankedset-intersection-update"]], "rnalysis.enrichment.RankedSet.isdisjoint": [[70, "rnalysis-enrichment-rankedset-isdisjoint"]], "rnalysis.enrichment.RankedSet.issubset": [[71, "rnalysis-enrichment-rankedset-issubset"]], "rnalysis.enrichment.RankedSet.issuperset": [[72, "rnalysis-enrichment-rankedset-issuperset"]], "rnalysis.enrichment.RankedSet.kegg_enrichment": [[73, "rnalysis-enrichment-rankedset-kegg-enrichment"]], "rnalysis.enrichment.RankedSet.non_categorical_enrichment": [[78, "rnalysis-enrichment-rankedset-non-categorical-enrichment"]], "rnalysis.enrichment.RankedSet.pop": [[79, "rnalysis-enrichment-rankedset-pop"]], "rnalysis.enrichment.RankedSet.remove": [[80, "rnalysis-enrichment-rankedset-remove"]], "rnalysis.enrichment.RankedSet.save_txt": [[81, "rnalysis-enrichment-rankedset-save-txt"]], "rnalysis.enrichment.RankedSet.single_set_enrichment": [[82, "rnalysis-enrichment-rankedset-single-set-enrichment"]], "rnalysis.enrichment.RankedSet.single_set_go_enrichment": [[83, "rnalysis-enrichment-rankedset-single-set-go-enrichment"]], "rnalysis.enrichment.RankedSet.symmetric_difference": [[85, "rnalysis-enrichment-rankedset-symmetric-difference"]], "rnalysis.enrichment.RankedSet.symmetric_difference_update": [[86, "rnalysis-enrichment-rankedset-symmetric-difference-update"]], "rnalysis.enrichment.RankedSet.translate_gene_ids": [[87, "rnalysis-enrichment-rankedset-translate-gene-ids"]], "rnalysis.enrichment.RankedSet.union": [[88, "rnalysis-enrichment-rankedset-union"]], "rnalysis.enrichment.RankedSet.update": [[89, "rnalysis-enrichment-rankedset-update"]], "rnalysis.enrichment.RankedSet.user_defined_enrichment": [[90, "rnalysis-enrichment-rankedset-user-defined-enrichment"]], "rnalysis.enrichment.enrichment_bar_plot": [[91, "rnalysis-enrichment-enrichment-bar-plot"]], "rnalysis.enrichment.gene_ontology_graph": [[92, "rnalysis-enrichment-gene-ontology-graph"]], "rnalysis.enrichment.kegg_pathway_graph": [[93, "rnalysis-enrichment-kegg-pathway-graph"]], "rnalysis.enrichment.upset_plot": [[94, "rnalysis-enrichment-upset-plot"]], "rnalysis.enrichment.venn_diagram": [[95, "rnalysis-enrichment-venn-diagram"]], "rnalysis.fastq.PairedEndPipeline": [[97, "rnalysis-fastq-pairedendpipeline"]], "rnalysis.fastq.PairedEndPipeline.add_function": [[98, "rnalysis-fastq-pairedendpipeline-add-function"]], "rnalysis.fastq.PairedEndPipeline.apply_to": [[99, "rnalysis-fastq-pairedendpipeline-apply-to"]], "rnalysis.fastq.PairedEndPipeline.export_pipeline": [[100, "rnalysis-fastq-pairedendpipeline-export-pipeline"]], "rnalysis.fastq.PairedEndPipeline.import_pipeline": [[101, "rnalysis-fastq-pairedendpipeline-import-pipeline"]], "rnalysis.fastq.PairedEndPipeline.remove_last_function": [[102, "rnalysis-fastq-pairedendpipeline-remove-last-function"]], "rnalysis.fastq.SingleEndPipeline": [[103, "rnalysis-fastq-singleendpipeline"]], "rnalysis.fastq.SingleEndPipeline.add_function": [[104, "rnalysis-fastq-singleendpipeline-add-function"]], "rnalysis.fastq.SingleEndPipeline.apply_to": [[105, "rnalysis-fastq-singleendpipeline-apply-to"]], "rnalysis.fastq.SingleEndPipeline.export_pipeline": [[106, "rnalysis-fastq-singleendpipeline-export-pipeline"]], "rnalysis.fastq.SingleEndPipeline.import_pipeline": [[107, "rnalysis-fastq-singleendpipeline-import-pipeline"]], "rnalysis.fastq.SingleEndPipeline.remove_last_function": [[108, "rnalysis-fastq-singleendpipeline-remove-last-function"]], "rnalysis.fastq.bowtie2_align_paired_end": [[109, "rnalysis-fastq-bowtie2-align-paired-end"]], "rnalysis.fastq.bowtie2_align_single_end": [[110, "rnalysis-fastq-bowtie2-align-single-end"]], "rnalysis.fastq.bowtie2_create_index": [[111, "rnalysis-fastq-bowtie2-create-index"]], "rnalysis.fastq.featurecounts_paired_end": [[116, "rnalysis-fastq-featurecounts-paired-end"]], "rnalysis.fastq.featurecounts_single_end": [[117, "rnalysis-fastq-featurecounts-single-end"]], "rnalysis.fastq.kallisto_create_index": [[119, "rnalysis-fastq-kallisto-create-index"]], "rnalysis.fastq.kallisto_quantify_paired_end": [[120, "rnalysis-fastq-kallisto-quantify-paired-end"]], "rnalysis.fastq.kallisto_quantify_single_end": [[121, "rnalysis-fastq-kallisto-quantify-single-end"]], "rnalysis.fastq.shortstack_align_smallrna": [[124, "rnalysis-fastq-shortstack-align-smallrna"]], "rnalysis.fastq.trim_adapters_paired_end": [[126, "rnalysis-fastq-trim-adapters-paired-end"]], "rnalysis.fastq.trim_adapters_single_end": [[127, "rnalysis-fastq-trim-adapters-single-end"]], "rnalysis.filtering": [[129, "rnalysis-filtering"]], "rnalysis.filtering.CountFilter": [[130, "rnalysis-filtering-countfilter"]], "rnalysis.filtering.CountFilter.average_replicate_samples": [[131, "rnalysis-filtering-countfilter-average-replicate-samples"]], "rnalysis.filtering.CountFilter.biotypes_from_gtf": [[132, "rnalysis-filtering-countfilter-biotypes-from-gtf"]], "rnalysis.filtering.CountFilter.biotypes_from_ref_table": [[133, "rnalysis-filtering-countfilter-biotypes-from-ref-table"]], "rnalysis.filtering.CountFilter.box_plot": [[134, "rnalysis-filtering-countfilter-box-plot"]], "rnalysis.filtering.CountFilter.clustergram": [[135, "rnalysis-filtering-countfilter-clustergram"]], "rnalysis.filtering.CountFilter.describe": [[136, "rnalysis-filtering-countfilter-describe"]], "rnalysis.filtering.CountFilter.difference": [[137, "rnalysis-filtering-countfilter-difference"]], "rnalysis.filtering.CountFilter.differential_expression_deseq2": [[138, "rnalysis-filtering-countfilter-differential-expression-deseq2"]], "rnalysis.filtering.CountFilter.differential_expression_limma_voom": 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"rnalysis.filtering.FoldChangeFilter.translate_gene_ids": [[331, "rnalysis-filtering-foldchangefilter-translate-gene-ids"]], "rnalysis.filtering.FoldChangeFilter.union": [[332, "rnalysis-filtering-foldchangefilter-union"]], "rnalysis.filtering.Pipeline": [[333, "rnalysis-filtering-pipeline"]], "rnalysis.filtering.Pipeline.add_function": [[334, "rnalysis-filtering-pipeline-add-function"]], "rnalysis.filtering.Pipeline.apply_to": [[335, "rnalysis-filtering-pipeline-apply-to"]], "rnalysis.filtering.Pipeline.export_pipeline": [[336, "rnalysis-filtering-pipeline-export-pipeline"]], "rnalysis.filtering.Pipeline.import_pipeline": [[337, "rnalysis-filtering-pipeline-import-pipeline"]], "rnalysis.filtering.Pipeline.remove_last_function": [[338, "rnalysis-filtering-pipeline-remove-last-function"]], "rnalysis.general": [[339, "rnalysis-general"]], "rnalysis.general.clear_all_cache": [[340, "rnalysis-general-clear-all-cache"]], "rnalysis.general.clear_gui_cache": [[341, "rnalysis-general-clear-gui-cache"]], "rnalysis.general.parse_gene_name_string": [[342, "rnalysis-general-parse-gene-name-string"]], "rnalysis.general.parse_sequence_name_string": [[343, "rnalysis-general-parse-sequence-name-string"]], "rnalysis.general.parse_wbgene_string": [[344, "rnalysis-general-parse-wbgene-string"]], "rnalysis.general.print_settings_file": [[345, "rnalysis-general-print-settings-file"]], "rnalysis.general.reset_settings_file": [[346, "rnalysis-general-reset-settings-file"]], "rnalysis.general.save_to_csv": [[347, "rnalysis-general-save-to-csv"]], "rnalysis.general.set_attr_ref_table_path": [[348, "rnalysis-general-set-attr-ref-table-path"]], "rnalysis.general.set_biotype_ref_table_path": [[349, "rnalysis-general-set-biotype-ref-table-path"]], "A-to-Z tutorial - example analysis": [[350, "a-to-z-tutorial-example-analysis"]], "Intro and recommendations": [[350, "intro-and-recommendations"]], "Analysis #1 - time series RNA sequencing": [[350, "analysis-1-time-series-rna-sequencing"]], "The dataset": [[350, "the-dataset"], [350, "id6"]], "Start RNAlysis": [[350, "start-rnalysis"]], "Data preprocessing and exploratory data analysis": [[350, "data-preprocessing-and-exploratory-data-analysis"]], "Filter out lowly-expressed genes": [[350, "filter-out-lowly-expressed-genes"]], "Examine variance in our data with Principal Component Analysis": [[350, "examine-variance-in-our-data-with-principal-component-analysis"]], "Examine similarity between developmental stages": [[350, "examine-similarity-between-developmental-stages"]], "Compare the expression of specific genes over the developmental stages": [[350, "compare-the-expression-of-specific-genes-over-the-developmental-stages"]], "Clustering analysis": [[350, "clustering-analysis"]], "The simple approach - distance-based clustering with K-Medoids": [[350, "the-simple-approach-distance-based-clustering-with-k-medoids"]], "Fine-tuning our approach - density-based clustering with HDBSCAN": [[350, "fine-tuning-our-approach-density-based-clustering-with-hdbscan"]], "The complex approach - ensemble-based clustering with CLICOM": [[350, "the-complex-approach-ensemble-based-clustering-with-clicom"]], "Enrichment analysis": [[350, "enrichment-analysis"], [350, "id9"], [352, "enrichment-analysis"]], "Running enrichment analysis": [[350, "running-enrichment-analysis"], [350, "id11"]], "Create analysis report": [[350, "create-analysis-report"]], "Analysis #2 - differential expression data": [[350, "analysis-2-differential-expression-data"]], "Quantify FASTQ files and Differential Expression Analysis": [[350, "quantify-fastq-files-and-differential-expression-analysis"]], "Quality control with FastQC": [[350, "quality-control-with-fastqc"]], "Trim adapters and remove low-quality reads with CutAdapt": [[350, "trim-adapters-and-remove-low-quality-reads-with-cutadapt"]], "Quantify gene expression with kallisto": [[350, "quantify-gene-expression-with-kallisto"]], "Run differential expression analysis with DESeq2": [[350, "run-differential-expression-analysis-with-deseq2"]], "Data filtering and visualization with customized Pipelines": [[350, "data-filtering-and-visualization-with-customized-pipelines"]], "Create a customized Pipeline": [[350, "create-a-customized-pipeline"]], "Apply the Pipeline to our datasets": [[350, "apply-the-pipeline-to-our-datasets"]], "Visualizing and extracting gene set interesctions": [[350, "visualizing-and-extracting-gene-set-interesctions"]], "Create a Venn diagram": [[350, "create-a-venn-diagram"]], "Extract the gene subsets we are interested in": [[350, "extract-the-gene-subsets-we-are-interested-in"]], "Define a background set": [[350, "define-a-background-set"]], "Define our custom enrichment attributes": [[350, "define-our-custom-enrichment-attributes"]], "Final words": [[350, "final-words"]], "User guide - programmatic interface": [[351, "user-guide-programmatic-interface"]], "RNAlysis fastq module": [[351, "rnalysis-fastq-module"]], "Working with the fastq module": [[351, "working-with-the-fastq-module"]], "Adapter trimming with CutAdapt": [[351, "adapter-trimming-with-cutadapt"]], "Single-end adapter trimming": [[351, "single-end-adapter-trimming"]], "Paired-end adapter trimming": [[351, "paired-end-adapter-trimming"]], "RNA sequencing quantification with kallisto": [[351, "rna-sequencing-quantification-with-kallisto"]], "Building or acquiring index files": [[351, "building-or-acquiring-index-files"], [351, "id2"]], "Single-end read quantification": [[351, "single-end-read-quantification"]], "Paired-end read quantification": [[351, "paired-end-read-quantification"]], "Read alignment with bowtie2": [[351, "read-alignment-with-bowtie2"]], "Single-end read alignment": [[351, "single-end-read-alignment"]], "Paired-end read alignment": [[351, "paired-end-read-alignment"]], "Feature counting with featureCounts": [[351, "feature-counting-with-featurecounts"]], "Single-end read feature counting": [[351, "single-end-read-feature-counting"]], "Paired-end read feature counting": [[351, "paired-end-read-feature-counting"]], "RNAlysis filtering module": [[351, "rnalysis-filtering-module"]], "Working with Filter objects": [[351, "working-with-filter-objects"]], "Initialize a Filter object": [[351, "initialize-a-filter-object"]], "View a Filter object": [[351, "view-a-filter-object"]], "Filtering operations": [[351, "filtering-operations"], [352, "filtering-operations"]], "Performing set operations on multiple Filter objects": [[351, "performing-set-operations-on-multiple-filter-objects"]], "Saving Filter results": [[351, "saving-filter-results"]], "Using an Attribute Reference Table for filter operations": [[351, "using-an-attribute-reference-table-for-filter-operations"]], "Using a Biotype Reference Table for filter operations": [[351, "using-a-biotype-reference-table-for-filter-operations"]], "Filtering DESeq2 output files with filtering.DESeqFilter": [[351, 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