AbundanceMetadata-class
                        AbundanceMetadata s4 class
BgeeCall                generate gene expression calls with BgeeCall
BgeeMetadata-class      BgeeMetadata S4 class
KallistoMetadata-class
                        KallistoMetadata S4 class
Pvalue_averaging        Pvalue averaging
UserMetadata-class      UserMetadata 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_initial_intergenic_regions
                        generates the initial intergenic regions
generate_presence_absence
                        Generate presence absence
generate_reference_intergenic_regions
                        Generates reference intergenic regions by
                        removing outlier intergenics
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
getIntergenicRelease    'intergenic_release' Getter
getRunIds               'run_ids' Getter
getSimpleArborescence   'simple_arborescence' Getter
getWorkingPath          'working_path' Getter
get_summary_stats       Gather statistical information
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
setAnnotationFromObject
                        Set annotation_object of one UserMetadata
                        object
setIntergenicRelease    'intergenic_release' Setter
setOutputDir            'output_dir' Setter
setRNASeqLibPath        'rnaseq_lib_path' Setter
setRunIds               'run_ids' Setter
setSimpleArborescence   'simple_arborescence' Setter
setTranscriptomeFromFile
                        Set transcriptome_object of one UserMetadata
                        object
setTranscriptomeFromObject
                        Set transcriptome_object of one UserMetadata
                        object
setWorkingPath          'working_path' Setter
