9de775ad072971380d5e14b1547d6265 *DESCRIPTION
6ee27b2996a745ecf00967b38da9c49a *LICENSE
156a4c34d4a1804d16c6c6a7016c4d28 *NAMESPACE
dbf7ed7bd76df42f1992fb608b109464 *R/AbundanceMetadata.R
32ac162ed4ce1abf4e941746613040c3 *R/BgeeCall.R
cac584b91380aa103e2ef5af96466a23 *R/BgeeMetadata.R
e990ea4ed6465f06540bf442175c7f86 *R/KallistoMetadata.R
3f2b11bd4aa41b0d29ba2334f56bbabe *R/UserMetadata.R
7fa38492978026b5f7dccbb6be4b73e8 *R/bgeePipelineFunctions.R
26f93d8b848307a2c215802aadfbcf87 *R/galaxyWrapper.R
9e950fb1804e78bb9c79900fc46f2429 *R/geneToBiotype.R
6953831c7a858c357e0d1a1adbf41556 *R/generateIntergenicRegions.R
2d123776333a3fb22ac728898f622db1 *R/getSummary.R
45ee9b347bb39f1f7241d4d158ac1345 *R/imports.R
76df3318b0537e32e3d4e1e8f99d3f92 *R/kallisto.R
886ec79fa5e7f048e09d031d9fc17b22 *R/listIntergenicRelease.R
a6fc5f0268d5b810138c3a735aff43ed *R/mergingLibraries.R
93a5f71e5dadd5539533d80863405a26 *R/prepareTranscriptome.R
84c7882a3c168467462ff0aa215d6ae9 *R/presenceAbsence.R
97b52eb38f935f6189e87a50b966bf4d *R/retrieveAnnotationTranscriptome.R
e04fea95e12b5c0cd387b8d0ac16ff1e *R/retrieveFromBgee.R
2965babd52acd0dac4341ce0499305b3 *R/retrieveFromCommunity.R
ca211db7c5eb07948bfc63fa3d4ab19d *R/retrievelibraries.R
0e2b90e5761314da902585ae8f7ab154 *R/runCallsPipeline.R
cee8c3faaeb6ba373e500530959b0bef *R/runCallsSlurm.R
4523dbc0109a78284417081fc9707487 *R/transcriptToBiotype.R
53addf5893570357e3615e10ada78671 *R/transcriptToGene.R
f772bff07e8b1901472d25e44a746054 *R/utils.R
c4133523fe2feb0bfb4b40db152d4a0c *README.md
bdf472d8c3aa5f17ace8e48bf2b35565 *build/vignette.rds
40540de1f70da1bbb72c4fb58b5f3733 *inst/NEWS.Rd
33161c398ca2551b0d003ef9512d6a3b *inst/doc/bgeecall-manual.R
661df5cac63ddf1aaf4ae68e5cab2bdf *inst/doc/bgeecall-manual.Rmd
e5c650a72725da0dd03578e87392e110 *inst/doc/bgeecall-manual.html
5672541e6cb270e1d384b5963b653b2a *inst/extdata/SRX099901_subset/SRR350955_subset.fastq.gz
6fa5ec7100a04a071ac43d9491ddcd81 *inst/extdata/annotation.gtf
973b3e5aa9d6d76c12969d8cdfcac179 *inst/extdata/intergenic_1.0/6239/annotation_WBcel235_84/gene2biotype.tsv
bb94eb38028b302c8fe67df61d99e883 *inst/extdata/intergenic_1.0/6239/annotation_WBcel235_84/tx2gene.tsv
94c6a78635d4a418ccad3a83b8a408d4 *inst/extdata/intergenic_1.0/all_results/SRX099901_subset/abundance.tsv
924379603da81869e738cdda477003ad *inst/extdata/transcriptome.fa
003f776c2a8dc8f771f061dbf10e448f *inst/userMetadataTemplate.tsv
74ed09d98ab12046b7591e9a2c4ace13 *inst/userMetadataTemplate_merging.tsv
d1a9e703265877648f1cbdb6faf2c506 *man/AbundanceMetadata-class.Rd
51b2fe468f235d543d4a55b13c755dcd *man/BgeeCall.Rd
b2b29c0b968bcfa0a94a20993cba2068 *man/BgeeMetadata-class.Rd
e024728e41586a2ace95c0d4643c2d37 *man/KallistoMetadata-class.Rd
8d15704f5a7f0196eeacadea57503e4d *man/Pvalue_averaging.Rd
dd5d16790a33fa1a7a8998d18e99dc17 *man/UserMetadata-class.Rd
99637a8a2231479ff2a2feaf42d3eb12 *man/create_kallisto_index.Rd
5adb7b33d8c75f64840b8f1768d88bf9 *man/download_fasta_intergenic.Rd
a92280fa76e2b028d9fa3b3b65230705 *man/download_kallisto.Rd
860430be3d10f8efe4f81fa5ced31fba *man/generate_calls_workflow.Rd
9fc968f518a42c0a2fc1dd4899053617 *man/generate_initial_intergenic_regions.Rd
5be96ff0f593bc8db970edfb5e471c52 *man/generate_presence_absence.Rd
ea687a38695d5a153046f721d41f55ca *man/generate_reference_intergenic_regions.Rd
11b71d540f53695bab4b3cbdc7d1cb14 *man/generate_slurm_calls.Rd
4ab8712019f972b873f3fe50b9c0f540 *man/generate_slurm_indexes.Rd
aa8fd8c156c8ed461b3ae0eb92fa3be1 *man/getIntergenicPrefix.Rd
76f62e0e9dcc4577d4d0c04dc3876508 *man/getIntergenicRelease.Rd
571b5e91e234c593fef8cfe61c35bdbb *man/getRunIds.Rd
74f0bd06d20470fa2e1f10fef21b933b *man/getSimpleArborescence.Rd
f1748ec3b5d0f03405436f6f13bc21c8 *man/getWorkingPath.Rd
f020892316ef0a849a75d08dfcdaea5c *man/get_summary_stats.Rd
e2411c626911be39532327fefede8f15 *man/list_bgee_ref_intergenic_species.Rd
6f7aa3fa3005e66664444eb92835491f *man/list_community_ref_intergenic_species.Rd
cecbf7d8583b105f8f1791cefc39c88d *man/list_intergenic_release.Rd
b945db8ab8a9446e2b9aa4690a228636 *man/merge_transcriptome_and_intergenic.Rd
d2fbf8c3a519246cfa0336aa9de0f97e *man/merging_libraries.Rd
844b4a10291fb861f4da8ec37b12287b *man/run_kallisto.Rd
6f1cb3c742a1eaa24bcf1be4bb8509db *man/run_tximport.Rd
fbc76f935028861a0de535f2ab94a303 *man/setAnnotationFromFile.Rd
72bf8d618cf3c61a546b7577c30d8e62 *man/setAnnotationFromObject.Rd
bc194a16030d9ed5db7d1b317639e677 *man/setIntergenicRelease.Rd
8a8f5ff4f30f38a22e89acec78bd5d8b *man/setOutputDir.Rd
130f3638a4acc671cfdfee8705a7c9ed *man/setRNASeqLibPath.Rd
70f7d422fd8f36190acefe416ab1ff90 *man/setRunIds.Rd
4d93ab76f0ba90c2308dd748feb6b371 *man/setSimpleArborescence.Rd
85dd571351a4eff82e12cfef4ff7f495 *man/setTranscriptomeFromFile.Rd
2b0caacdbed8c890a53312ed3f52f9b9 *man/setTranscriptomeFromObject.Rd
075bc9935609cb44e732e9dff2fda440 *man/setWorkingPath.Rd
b428b0f90ffd2b1b46927ad59d83a532 *tests/testthat.R
ecadee6148c4edf7ea1277b6b818d705 *tests/testthat/test_geneToBiotype.R
ff0928de7c4928094c9198538f048d9a *tests/testthat/test_kallisto.R
1bc3d9e6f7d925f42655a72a014d4e5c *tests/testthat/test_prepareTranscriptome.R
7aaf34b43c7d84a4d4630dec8fc7d72a *tests/testthat/test_transcriptToBiotype.R
eaf9faba3c86a238a6c6c20151d8ed64 *tests/testthat/test_transcriptToGene.R
b627b35bb31cdb1a48c1bda09d3d5e7c *tests/testthat/testdata/kallisto/abundance.tsv
661df5cac63ddf1aaf4ae68e5cab2bdf *vignettes/bgeecall-manual.Rmd
