Files in BgeeCall
Automatic RNA-Seq present/absent gene expression calls generation
NAMESPACE
DESCRIPTION
README.md
tests/testthat.R
tests/testthat/test_transcriptToBiotype.R
tests/testthat/test_kallisto.R
tests/testthat/test_prepareTranscriptome.R
tests/testthat/test_transcriptToGene.R
tests/testthat/test_geneToBiotype.R
tests/testthat/testdata/kallisto/abundance.tsv
R/retrieveFromCommunity.R
R/BgeeMetadata.R
R/utils.R
R/kallisto.R
R/runCallsPipeline.R
R/transcriptToBiotype.R
R/UserMetadata.R
R/prepareTranscriptome.R
R/retrieveFromBgee.R
R/AbundanceMetadata.R
R/geneToBiotype.R
R/listIntergenicRelease.R
R/BgeeCall.R
R/KallistoMetadata.R
R/runCallsSlurm.R
R/transcriptToGene.R
R/presenceAbsence.R
R/bgeePipelineFunctions.R
man/download_fasta_intergenic.Rd
man/run_tximport.Rd
man/setIntergenicRelease.Rd
man/setRNASeqLibPath.Rd
man/UserMetadata-class.Rd
man/generate_presence_absence.Rd
man/setRunIds.Rd
man/getRunIds.Rd
man/setAnnotationFromFile.Rd
man/download_kallisto.Rd
man/BgeeMetadata-class.Rd
man/setTranscriptomeFromObject.Rd
man/generate_slurm_calls.Rd
man/list_intergenic_release.Rd
man/generate_slurm_indexes.Rd
man/list_community_ref_intergenic_species.Rd
man/KallistoMetadata-class.Rd
man/setTranscriptomeFromFile.Rd
man/merge_transcriptome_and_intergenic.Rd
man/setAnnotationFromObject.Rd
man/getIntergenicPrefix.Rd
man/list_bgee_ref_intergenic_species.Rd
man/generate_calls_workflow.Rd
man/getIntergenicRelease.Rd
man/AbundanceMetadata-class.Rd
man/setOutputDir.Rd
man/setSimpleArborescence.Rd
man/getSimpleArborescence.Rd
man/create_kallisto_index.Rd
man/BgeeCall.Rd
man/setWorkingPath.Rd
man/run_kallisto.Rd
man/getWorkingPath.Rd
inst/userMetadataTemplate.tsv
inst/NEWS.Rd
inst/extdata/transcriptome.fa
inst/extdata/annotation.gtf
inst/extdata/intergenic_0.1/all_results/SRX099901_subset/abundance.tsv
inst/extdata/intergenic_0.1/6239/annotation_WBcel235_84/tx2gene.tsv
inst/extdata/intergenic_0.1/6239/annotation_WBcel235_84/gene2biotype.tsv
inst/extdata/SRX099901_subset/SRR350955_subset.fastq.gz
inst/doc/bgeecall-manual.R
inst/doc/bgeecall-manual.Rmd
inst/doc/bgeecall-manual.html
build/vignette.rds
vignettes/bgeecall-manual.Rmd
