4a8a04b78ad6c9ff5a7a931c0d30e6fc *DESCRIPTION
5bc85dcbff3857b9837b5636612be07d *NAMESPACE
789c228f1ac7b9b36d5da18e640923e7 *R/analyze_ORF.R
4d4ffe074f69a263dda45b54dcc4a602 *R/analyze_alternative_splicing.R
9ac52f9319af149cf9aec254308317fe *R/analyze_external_sequence_analysis.R
e0664ae757097cfe398d11b101f501b3 *R/analyze_switch_consequences.R
5abda98d8fa4c7868f0196135ebc7475 *R/classes.R
32f6c1f82149cee44aa56a722fe16eb8 *R/high_level_functions.R
8575654203e30efc6c235a7df5d1dc8d *R/import_data.R
29468dd7ee15bf2013985d6bd8c5d678 *R/isoform_plots.R
7c8b3c191d8a4650680452e564a8823b *R/methods.R
ff963a73a779bf63617e5f74633c178b *R/plot_all_iso_switch.R
dc9c0f73e3de9e818a6f7945de837d5d *R/test_isoform_switches.R
3c80fd3d203d6dafda1fbea4263adb4b *R/tools.R
2465e5e72e2c6cb83699fce9aed888f5 *README.md
3af31988c6c5725a38c020faf9bb240c *build/vignette.rds
06ae17cd69543c37f30c60ae2b6271dc *data/datalist
4c5ecca0b916ea98404c02f2c9c0a1e6 *data/exampleSwitchList.RData
cd9758b17cdf9edb226168f765e0cdcb *data/exampleSwitchListAnalyzed.RData
f05bf833be7f873f902b8bcbfa883b14 *data/exampleSwitchListIntermediary.RData
17f65e4e47f61b34862c3845e4306dda *inst/CITATION
72e542af4dd41278228e535b2aa09c6e *inst/NEWS
0835b80e6b6fdd582b414ee315701250 *inst/doc/IsoformSwitchAnalyzeR.R
c3e45028947feb8d04443b42f14c80dd *inst/doc/IsoformSwitchAnalyzeR.Rmd
3f05095fb5506334d69e0d675ce17d3e *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
e17eb9af63905778e8aa1f42087674f7 *inst/extdata/deeploc21.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
ebe54fbbe4651206a8d4d5190726f461 *inst/extdata/interproscan_results.json.gz
e98470eb3aecfbdfe103d9f84f664a98 *inst/extdata/iupred2a_result.txt.gz
3b0ac8821d66aa9dc919a6349af678ca *inst/extdata/netsurfp3_result.csv.gz
35a0ad8b972eae13b1f3ed93def3ffac *inst/extdata/pfam_results.txt
4ca4d15ca4df68ec2f050a2da4d07459 *inst/extdata/predefined_switches_example.tsv
4dd7742df326629fab430a7a06b05e91 *inst/extdata/predefined_switches_example_no_qvalue.tsv
eb099ce30b3c2c45b9c905428a0878b7 *inst/extdata/signalP_results.txt
695ecd7f3d91983a3a0fe1b99bdad65c *man/IsoformSwitchTestDEXSeq.Rd
600550f5fb87b8c69bc619c4999dc487 *man/IsoformSwitchTestSatuRn.Rd
3d4f279d9e7ea254aadc08dbf76cf98b *man/addORFfromGTF.Rd
87dbeca2c77d52fdafe24223518695da *man/analyzeAlternativeSplicing.Rd
fbe3a2c6aa47ec6f8db193d6f7df8175 *man/analyzeCPAT.Rd
b75115e7cbe5748ce4090ce296730e97 *man/analyzeCPC2.Rd
af30183c2e196fcb61362d8de5fdc464 *man/analyzeDeepLoc2.Rd
5c814ff237ecabdd535ca8082a3511e8 *man/analyzeDeepTMHMM.Rd
9ab4e5111fe2ba17a9b9aaec7cd99c03 *man/analyzeIUPred2A.Rd
f9759f1831eb1fb705d0ef10c304a751 *man/analyzeInterProScan.Rd
868f0b078356e0840ac6322cbbc9a72e *man/analyzeNetSurfP3.Rd
0a23e5eb1859f47349ec619845266e90 *man/analyzeNovelIsoformORF.Rd
76d21f22b853f2e2e06ef6398bdc9a44 *man/analyzeORF.Rd
e027a2be2a16d888e6ef571b52c79604 *man/analyzePFAM.Rd
08f26162ed7f5f0b47cbfd36ce0e8ee0 *man/analyzeSignalP.Rd
38106781869b107a6d52ce8e8943bacd *man/analyzeSwitchConsequences.Rd
c9bf079affbb2a44b6f5327d640e7677 *man/exportToPairedGSEA.Rd
8d6436e2e701efd4eaab401b95e08d07 *man/expressionAnalysisPlots.Rd
b94c20f3c4086f764ead888cc812b527 *man/extractConsequenceEnrichment.Rd
beb3d5d3ae993f5fac559422c3df8b66 *man/extractConsequenceEnrichmentComparison.Rd
22e5d27178e67509193f5c5c7eb7986d *man/extractConsequenceSummary.Rd
1e50e3b7add398af6d91c5689d6ce06a *man/extractGeneExpression.Rd
6a2a2f8598728941475040359445dc86 *man/extractGenomeWideAnalysis.Rd
13f827af2a5ed0545859ae69d904040a *man/extractGenomeWideSplicingAnalysis.Rd
ec8ac11b1479f0c6105b1ab0c2a665e1 *man/extractSequence.Rd
382af66fa4d74f5aa11f7836d93d2d9e *man/extractSplicingEnrichment.Rd
4f806210e7c56c8df7989dd5956dd320 *man/extractSplicingEnrichmentComparison.Rd
a809ad3aa2f0857a36eff182bd8d8f8f *man/extractSplicingSummary.Rd
f1cecbfd9b47c70acd827579219ed851 *man/extractSubCellShifts.Rd
efc048b23ab7e19fb5f282d9e2cdbd4a *man/extractSwitchOverlap.Rd
d143ad54944c62cd2fec7a4d8cdd333d *man/extractSwitchSummary.Rd
0606debbcf58467bca07118c3cf5c2b1 *man/extractTopSwitches.Rd
fb2245ef0dea2d25223f06d9dd8bc596 *man/importCufflinksFiles.Rd
319439d3bbd1bc55567ca12c1c53f56d *man/importGTF.Rd
15d08f9a16f395796b275c7cd67a08ec *man/importIsoformExpression.Rd
0321099d08142ddedfa8a72667d6d3e8 *man/importPairedGSEA.Rd
a1aebc2cf0755d1cd042c8061ed929ff *man/importPredefinedSwitches.Rd
8467c162cc5ad086f4bf20442e18c2d2 *man/importRdata.Rd
9dddbafee6289bb8aae01c8a46661b35 *man/importSalmonData.Rd
f943d14397723c72a661db232256927c *man/isoformSwitchAnalysisCombined.Rd
a58053d906a4bd7666054112a2990786 *man/isoformSwitchAnalysisPart1.Rd
b2ee07028bf9dfcb88f64ccc9e428d56 *man/isoformSwitchAnalysisPart2.Rd
24f9ca458ceaf9d046f42c54360a1a51 *man/isoformToGeneExp.Rd
38860a3e7454324d4a76b98bb407b71f *man/isoformToIsoformFraction.Rd
818eabc0a5f18d78a9e20ef8c67ed7cd *man/preFilter.Rd
fba0c7c5735ffb653f3e6e43acaeabd4 *man/prepareSalmonFileDataFrame.Rd
90551daf7cab9d4979147f678aa28f72 *man/subsetSwitchAnalyzeRlist.Rd
1c25b9a51c83eec9effb210e8715b707 *man/switchAnalyzeRlist.Rd
b3f3298d51c73fce7ee9cadd9049c392 *man/switchPlot.Rd
ed5b98ff87ece3e7c901267c6129f7dd *man/switchPlotTopSwitches.Rd
4701711d9f65afd724ec379492241064 *man/switchPlotTranscript.Rd
916c704d5461234fd4015ce5e08098bc *man/testData.Rd
a275ecb58458a266b3496626e7930b04 *src/utils.c
c3e45028947feb8d04443b42f14c80dd *vignettes/IsoformSwitchAnalyzeR.Rmd
97666c1cf65a9e36e0eed25206b1455d *vignettes/Overview_figure_detailed.jpg
84628cabc9e6143bfcb072604d38baad *vignettes/Overview_figure_simple.jpg
