# Automatic RNA-Seq present/absent gene expression calls generation

## Documentation for package ‘BgeeCall’ version 1.24.1

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

## Help Pages

BgeeCall-package | generate gene expression calls with BgeeCall
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_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
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
Pvalue_averaging | Pvalue averaging
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