Automatic RNA-Seq present/absent gene expression calls generation

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Documentation for package ‘BgeeCall’ version 1.16.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

AbundanceMetadata	AbundanceMetadata s4 class
AbundanceMetadata-class	AbundanceMetadata s4 class
BgeeCall	generate gene expression calls with BgeeCall
BgeeMetadata	BgeeMetadata S4 class
BgeeMetadata-class	BgeeMetadata S4 class
create_kallisto_index	Create kallisto indexes.
download_fasta_intergenic	Download fasta intergenic
download_kallisto	Download binary version of kallisto.
generate_calls_workflow	generate present/absent calls
generate_presence_absence	Generate presence absence
generate_slurm_calls	Generate present/absent calls on slurm queuing system
generate_slurm_indexes	Generate all indexes for the abundance quantification step
getIntergenicPrefix	'intergenic_prefix' Getter
getIntergenicPrefix,bgeeMetadata	'intergenic_prefix' Getter
getIntergenicPrefix-method	'intergenic_prefix' Getter
getIntergenicRelease	'intergenic_release' Getter
getIntergenicRelease,bgeeMetadata	'intergenic_release' Getter
getIntergenicRelease-method	'intergenic_release' Getter
getRunIds	'run_ids' Getter
getRunIds,userMetadata	'run_ids' Getter
getRunIds-method	'run_ids' Getter
getSimpleArborescence	'simple_arborescence' Getter
getSimpleArborescence,userMetadata	'simple_arborescence' Getter
getSimpleArborescence-method	'simple_arborescence' Getter
getWorkingPath	'working_path' Getter
getWorkingPath,userMetadata	'working_path' Getter
getWorkingPath-method	'working_path' Getter
get_summary_stats	Gather statistical information
KallistoMetadata	KallistoMetadata S4 class
KallistoMetadata-class	KallistoMetadata S4 class
list_bgee_ref_intergenic_species	List species having Bgee reference intergenic sequences
list_community_ref_intergenic_species	List species having reference intergenic sequences created by the BgeeCall community
list_intergenic_release	List reference intergenic releases usable with the BgeeCall package
merge_transcriptome_and_intergenic	Merge transcriptome file provided by the user with the Bgee intergenic fasta file.
merging_libraries	Calls of expression in combined libraries
run_kallisto	Run one kallisto abundance analyse
run_tximport	Run tximport
setAnnotationFromFile	Set annotation_object of one UserMetadata object
setAnnotationFromFile,userMetadata,character,character	Set annotation_object of one UserMetadata object
setAnnotationFromFile-method	Set annotation_object of one UserMetadata object
setAnnotationFromObject	Set annotation_object of one UserMetadata object
setAnnotationFromObject,userMetadata,GRanges,character	Set annotation_object of one UserMetadata object
setAnnotationFromObject-method	Set annotation_object of one UserMetadata object
setIntergenicRelease	'intergenic_release' Setter
setIntergenicRelease,bgeeMetadata,character	'intergenic_release' Setter
setIntergenicRelease-method	'intergenic_release' Setter
setOutputDir	'output_dir' Setter
setOutputDir,userMetadata,character	'output_dir' Setter
setOutputDir-method	'output_dir' Setter
setRNASeqLibPath	'rnaseq_lib_path' Setter
setRNASeqLibPath,userMetadata,character	'rnaseq_lib_path' Setter
setRNASeqLibPath-method	'rnaseq_lib_path' Setter
setRunIds	'run_ids' Setter
setRunIds,userMetadata,character	'run_ids' Setter
setRunIds-method	'run_ids' Setter
setSimpleArborescence	'simple_arborescence' Setter
setSimpleArborescence,userMetadata,logical	'simple_arborescence' Setter
setSimpleArborescence-method	'simple_arborescence' Setter
setTranscriptomeFromFile	Set transcriptome_object of one UserMetadata object
setTranscriptomeFromFile,userMetadata,character,character	Set transcriptome_object of one UserMetadata object
setTranscriptomeFromFile,userMetadata,character,missing	Set transcriptome_object of one UserMetadata object
setTranscriptomeFromFile-method	Set transcriptome_object of one UserMetadata object
setTranscriptomeFromObject	Set transcriptome_object of one UserMetadata object
setTranscriptomeFromObject,userMetadata,DNAStringSet,character	Set transcriptome_object of one UserMetadata object
setTranscriptomeFromObject-method	Set transcriptome_object of one UserMetadata object
setWorkingPath	'working_path' Setter
setWorkingPath,userMetadata,character	'working_path' Setter
setWorkingPath-method	'working_path' Setter
UserMetadata	UserMetadata S4 class
UserMetadata-class	UserMetadata S4 class