BgeeCall-package	BgeeCall
AbundanceMetadata	AbundanceMetadata-class
AbundanceMetadata-class	AbundanceMetadata-class
BgeeCall	BgeeCall
BgeeMetadata	BgeeMetadata-class
BgeeMetadata-class	BgeeMetadata-class
create_kallisto_index	create_kallisto_index
download_fasta_intergenic	download_fasta_intergenic
download_kallisto	download_kallisto
generate_calls_workflow	generate_calls_workflow
generate_initial_intergenic_regions	generate_initial_intergenic_regions
generate_presence_absence	generate_presence_absence
generate_reference_intergenic_regions	generate_reference_intergenic_regions
generate_slurm_calls	generate_slurm_calls
generate_slurm_indexes	generate_slurm_indexes
getIntergenicPrefix	getIntergenicPrefix
getIntergenicPrefix,bgeeMetadata	getIntergenicPrefix
getIntergenicPrefix,BgeeMetadata-method	getIntergenicPrefix
getIntergenicRelease	getIntergenicRelease
getIntergenicRelease,bgeeMetadata	getIntergenicRelease
getIntergenicRelease,BgeeMetadata-method	getIntergenicRelease
getRunIds	getRunIds
getRunIds,userMetadata	getRunIds
getRunIds,UserMetadata-method	getRunIds
getSimpleArborescence	getSimpleArborescence
getSimpleArborescence,userMetadata	getSimpleArborescence
getSimpleArborescence,UserMetadata-method	getSimpleArborescence
getWorkingPath	getWorkingPath
getWorkingPath,userMetadata	getWorkingPath
getWorkingPath,UserMetadata-method	getWorkingPath
get_summary_stats	get_summary_stats
KallistoMetadata	KallistoMetadata-class
KallistoMetadata-class	KallistoMetadata-class
list_bgee_ref_intergenic_species	list_bgee_ref_intergenic_species
list_community_ref_intergenic_species	list_community_ref_intergenic_species
list_intergenic_release	list_intergenic_release
merge_transcriptome_and_intergenic	merge_transcriptome_and_intergenic
merging_libraries	merging_libraries
Pvalue_averaging	Pvalue_averaging
run_kallisto	run_kallisto
run_tximport	run_tximport
setAnnotationFromFile	setAnnotationFromFile
setAnnotationFromFile,userMetadata,character,character	setAnnotationFromFile
setAnnotationFromFile,UserMetadata,character,character-method	setAnnotationFromFile
setAnnotationFromFile,UserMetadata,character,missing-method	setAnnotationFromFile
setAnnotationFromObject	setAnnotationFromObject
setAnnotationFromObject,userMetadata,GRanges,character	setAnnotationFromObject
setAnnotationFromObject,UserMetadata,GRanges,character-method	setAnnotationFromObject
setIntergenicRelease	setIntergenicRelease
setIntergenicRelease,bgeeMetadata,character	setIntergenicRelease
setIntergenicRelease,BgeeMetadata,character-method	setIntergenicRelease
setOutputDir	setOutputDir
setOutputDir,userMetadata,character	setOutputDir
setOutputDir,UserMetadata,character-method	setOutputDir
setRNASeqLibPath	setRNASeqLibPath
setRNASeqLibPath,userMetadata,character	setRNASeqLibPath
setRNASeqLibPath,UserMetadata,character-method	setRNASeqLibPath
setRunIds	setRunIds
setRunIds,userMetadata,character	setRunIds
setRunIds,UserMetadata,character-method	setRunIds
setSimpleArborescence	setSimpleArborescence
setSimpleArborescence,userMetadata,logical	setSimpleArborescence
setSimpleArborescence,UserMetadata,logical-method	setSimpleArborescence
setTranscriptomeFromFile	setTranscriptomeFromFile
setTranscriptomeFromFile,userMetadata,character,character	setTranscriptomeFromFile
setTranscriptomeFromFile,UserMetadata,character,character-method	setTranscriptomeFromFile
setTranscriptomeFromFile,userMetadata,character,missing	setTranscriptomeFromFile
setTranscriptomeFromFile,UserMetadata,character,missing-method	setTranscriptomeFromFile
setTranscriptomeFromObject	setTranscriptomeFromObject
setTranscriptomeFromObject,userMetadata,DNAStringSet,character	setTranscriptomeFromObject
setTranscriptomeFromObject,UserMetadata,DNAStringSet,character-method	setTranscriptomeFromObject
setWorkingPath	setWorkingPath
setWorkingPath,userMetadata,character	setWorkingPath
setWorkingPath,UserMetadata,character-method	setWorkingPath
UserMetadata	UserMetadata-class
UserMetadata-class	UserMetadata-class
