Files in BgeeCall

Automatic RNA-Seq present/absent gene expression calls generation

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 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/doc/bgeecall-manual.R inst/doc/bgeecall-manual.Rmd vignettes/bgeecall-manual.Rmd