cd3c5b22462360c1b83552fb2d3a8c2e *DESCRIPTION
69616f9914c865acbfd803f42e96e33a *NAMESPACE
b54fb38fea2c324c07dad19d2ee1592d *R/analyze_ORF.R
22279dc461ae33831659c71e217de8d1 *R/analyze_alternative_splicing.R
4750ec5294f26b356efa8b53ccc7f82a *R/analyze_external_sequence_analysis.R
f111016307d2f13b23f1a85081247232 *R/analyze_switch_consequences.R
5abda98d8fa4c7868f0196135ebc7475 *R/classes.R
f24ddcc2ec1409facd48890001afba21 *R/high_level_functions.R
2ffd31970e326ab128c9ebff9c32a7fb *R/import_data.R
0b3b846472f5599bb84a04888bb4e03e *R/isoform_plots.R
6c369da3602c2886a2effa3a658d4da7 *R/methods.R
5eae3370c6fb97d1901158b7bc184067 *R/plot_all_iso_switch.R
e7d999fba9fca5d1c1f5a4c58bc5b4bc *R/test_isoform_switches.R
8dd3c8e8ba9c6d18a870aeeed52c5b40 *R/tools.R
19ecc1c6dff4372dac5558c8aafac020 *README.md
97e7852339404e73333e66a9aaf81346 *build/vignette.rds
06ae17cd69543c37f30c60ae2b6271dc *data/datalist
710fb32502bfbd30d6fb2e6c9c20198c *data/exampleSwitchList.RData
40dbcd9255c27802590beb8539edaca4 *data/exampleSwitchListAnalyzed.RData
f05bf833be7f873f902b8bcbfa883b14 *data/exampleSwitchListIntermediary.RData
ad83a68a5f59ee491678b5eb1ad2b5d1 *inst/CITATION
fadc15c87a52b289dc6f24b6421c9d72 *inst/NEWS
244f86710157039cc3b8ad7baa3ce5e9 *inst/doc/IsoformSwitchAnalyzeR.R
3044e70c09b0ce2dd8ad867dd5bb190a *inst/doc/IsoformSwitchAnalyzeR.Rmd
7f6942c6cecbcbbcc7317a5bc1dacc08 *inst/doc/IsoformSwitchAnalyzeR.html
2714d7f8ed76bab7476754fbd20ade26 *inst/extdata/DeepTMHMM.gff3
e1a45c20f9f062fa408f8501e4efcbec *inst/extdata/Fibroblasts_0/quant.sf.gz
4d48de7347a408c5fc55b3eb6f68293a *inst/extdata/Fibroblasts_1/quant.sf.gz
902ec0aade084ab24c105a4591836b8d *inst/extdata/cpat_results.txt
fc899d7c76843c96da7e4a0898ffdd65 *inst/extdata/cpc2_result.txt
4e340e04ad9a37ec267e131a886ab6f5 *inst/extdata/deeploc2.csv
25f4c3c79e6b2febd3d08c9b50a27f3a *inst/extdata/drosophila/data_cond1_rep1/aux_info/meta_info.json
51944d89959cd8f2e85444dba98eb40b *inst/extdata/drosophila/data_cond1_rep1/cmd_info.json
39b5d8cec8aced9dcaae0d6c44f2b13a *inst/extdata/drosophila/data_cond1_rep1/quant.sf.gz
25f4c3c79e6b2febd3d08c9b50a27f3a *inst/extdata/drosophila/data_cond1_rep2/aux_info/meta_info.json
51944d89959cd8f2e85444dba98eb40b *inst/extdata/drosophila/data_cond1_rep2/cmd_info.json
a2dbae32e5cccf48ea4dedf1cd19ac0b *inst/extdata/drosophila/data_cond1_rep2/quant.sf.gz
25f4c3c79e6b2febd3d08c9b50a27f3a *inst/extdata/drosophila/data_cond2_rep1/aux_info/meta_info.json
51944d89959cd8f2e85444dba98eb40b *inst/extdata/drosophila/data_cond2_rep1/cmd_info.json
2ecf074320e917f372175f5e5148a37a *inst/extdata/drosophila/data_cond2_rep1/quant.sf.gz
25f4c3c79e6b2febd3d08c9b50a27f3a *inst/extdata/drosophila/data_cond2_rep2/aux_info/meta_info.json
51944d89959cd8f2e85444dba98eb40b *inst/extdata/drosophila/data_cond2_rep2/cmd_info.json
7d4b59f00c4368424b6b58295ddd1ec0 *inst/extdata/drosophila/data_cond2_rep2/quant.sf.gz
035cb397a213d53b813acaaf148028d3 *inst/extdata/example.gtf.gz
5026dc8e31a716c9ff3f9498c765ebd6 *inst/extdata/example_isoform_nt.fasta.gz
cd7d69a54bb3a6fbc825e50a884032a9 *inst/extdata/hESC_0/quant.sf.gz
f009f533ed0986620972818a2d1a46b6 *inst/extdata/hESC_1/quant.sf.gz
d7b2930ff02e3ab60fc63ca5a960e87f *inst/extdata/iPS_0/quant.sf.gz
8b9e7e28523460629e395a1524595766 *inst/extdata/iPS_1/quant.sf.gz
e98470eb3aecfbdfe103d9f84f664a98 *inst/extdata/iupred2a_result.txt.gz
35a0ad8b972eae13b1f3ed93def3ffac *inst/extdata/pfam_results.txt
eb099ce30b3c2c45b9c905428a0878b7 *inst/extdata/signalP_results.txt
23de9a230b2eff7eb4c2ba3e744e41a6 *man/IsoformSwitchTestDEXSeq.Rd
508c9d3d7be4c533c3f91742a3790e3c *man/IsoformSwitchTestSatuRn.Rd
9f477e7d70d1398396a36a45f9128b54 *man/addORFfromGTF.Rd
fbc89eec8880ec38c08011e35d846fe0 *man/analyzeAlternativSplicing.Rd
a133354c3813e3bf217799d06ac7e9f0 *man/analyzeCPAT.Rd
5ed42a60e955431d1cc754e26b3f5e01 *man/analyzeCPC2.Rd
fce9c35e9096c31f0a2b0ba0635b7354 *man/analyzeDeepLoc2.Rd
c1f0bb2a59e353af6f3bb1072499dceb *man/analyzeDeepTMHMM.Rd
4b4c9817ef8ffc93660c137bd2472144 *man/analyzeIUPred2A.Rd
48234fb74da28644dee7ba25b2aa73fc *man/analyzeNetSurf2.Rd
53b2ae2e42da10a3deef0b326d0a0bfb *man/analyzeNovelIsoformORF.Rd
8130468c2bb3785774fc9d5784eb754e *man/analyzeORF.Rd
fb06a711c8129cf57dc7353efcf65520 *man/analyzePFAM.Rd
f8d309bf1c58fd80a1c8cb8a0404f5a8 *man/analyzeSignalP.Rd
ead0d60fbf02dd3cc17a17f24b94b5b2 *man/analyzeSwitchConsequences.Rd
05c199cc5c28e379f073010992102bdc *man/expressionAnalysisPlots.Rd
ec69485fcd0c294b177acb4c1a39eeff *man/extractConsequenceEnrichment.Rd
4cb2718c51f49db47b36c4f227b55d94 *man/extractConsequenceEnrichmentComparison.Rd
34cfaac015641a78d4972cd1ade8a3a1 *man/extractConsequenceSummary.Rd
8d6577174167d16c57982f0938893345 *man/extractGeneExpression.Rd
a4b6bf1a2b5bd14d8241b95de6365051 *man/extractGenomeWideAnalysis.Rd
32cf9b2429d44d1d40be9474efed9aaf *man/extractGenomeWideSplicingAnalysis.Rd
c009c557b5489752ea525f4a079529f9 *man/extractSequence.Rd
981a3c8c6f79f9670e8ec4cacab57c7b *man/extractSplicingEnrichment.Rd
65af574368992212c3421dcef5308fb0 *man/extractSplicingEnrichmentComparison.Rd
2325de38038437cb6da10a461d555bd1 *man/extractSplicingSummary.Rd
ca5af58befc8d3f534a054d58d1b2fd1 *man/extractSubCellShifts.Rd
fe53b766a4f2f69130e84a4d38121abc *man/extractSwitchOverlap.Rd
798200e062ef6d156fe6e4ab2ab71f6c *man/extractSwitchSummary.Rd
446e29dadf2638690583ddf47fc41115 *man/extractTopSwitches.Rd
3b728d5c641ab3148d11781f7da7cc4a *man/importCufflinksGalaxyData.Rd
6e93cd791427c8d92916827eb7db7517 *man/importGTF.Rd
4db6c3923a6e551f98e367900b570fc2 *man/importIsoformExpression.Rd
6f41ab1a102a2eeb7f91832b297fb7d8 *man/importRdata.Rd
c6517a35bef583a9e68f77980a1291ee *man/importSalmonData.Rd
d2f5347801d5fd29a7fcae0c6f7e4071 *man/isoformSwitchAnalysisCombined.Rd
11df889d80748cd87d9289fb0f9d1beb *man/isoformSwitchAnalysisPart1.Rd
44e95859bd318f1cdc268fb1639323b9 *man/isoformSwitchAnalysisPart2.Rd
c2ab025c4ca27c4ba8734676cc0dea8b *man/isoformToGeneExp.Rd
4f05635f1a6b4b3a5a83adb068232eb7 *man/isoformToIsoformFraction.Rd
32ba4fc2b68c23675430e4a81e1a6630 *man/preFilter.Rd
bf91d821fa3aca67d704011acb4ff601 *man/prepareSalmonFilesDataFrame.Rd
c0eca61d6c6150bae23707f326425eec *man/subsetSwitchAnalyzeRlist.Rd
a3f9d5e2374b39a09a8cdd5d3176c566 *man/switchAnalyzeRlist.Rd
bec464a24c94ef86c26fe296b8ee9653 *man/switchPlot.Rd
db1c3d53720c98c13fcfee8d351b9a6d *man/switchPlotTopSwitches.Rd
3b555371703a5f100face7112ff8e838 *man/switchPlotTranscript.Rd
a01f082ed3cd961d2dae7ea0693cb826 *man/testData.Rd
a275ecb58458a266b3496626e7930b04 *src/utils.c
3044e70c09b0ce2dd8ad867dd5bb190a *vignettes/IsoformSwitchAnalyzeR.Rmd
97666c1cf65a9e36e0eed25206b1455d *vignettes/Overview_figure_detailed.jpg
84628cabc9e6143bfcb072604d38baad *vignettes/Overview_figure_simple.jpg
