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

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Functions
125
Source code
25
Man pages
33
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BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation
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API

API for BgeeCall
Automatic RNA-Seq present/absent gene expression calls generation

Global functions
AbundanceMetadata Man page
AbundanceMetadata-class Man page
BgeeCall Man page
BgeeMetadata Man page
BgeeMetadata-class Man page
KallistoMetadata Man page
KallistoMetadata-class Man page
UserMetadata Man page
UserMetadata-class Man page
abundance_without_intergenic Source code
calculate_abundance_cutoff Source code
check_run_ids Source code
countToTpm Source code
create_TxDb Source code
create_gene_to_biotype Source code
create_kallisto_index Man page Source code
create_tx2gene Source code
cutoff_info Source code
download_fasta_intergenic Man page Source code
download_kallisto Man page Source code
generateRScriptPath Source code
generate_S4_object_properties_output Source code
generate_calls_workflow Man page Source code
generate_presence_absence Man page Source code
generate_slurm_calls Man page Source code
generate_slurm_indexes Man page Source code
getIntergenicPrefix Man page
getIntergenicPrefix,BgeeMetadata-method Man page
getIntergenicPrefix,bgeeMetadata Man page
getIntergenicRelease Man page
getIntergenicRelease,BgeeMetadata-method Man page
getIntergenicRelease,bgeeMetadata Man page
getRunIds Man page
getRunIds,UserMetadata-method Man page
getRunIds,userMetadata Man page
getSimpleArborescence Man page
getSimpleArborescence,UserMetadata-method Man page
getSimpleArborescence,userMetadata Man page
getWorkingPath Man page
getWorkingPath,UserMetadata-method Man page
getWorkingPath,userMetadata Man page
get_abundance_file_path Source code
get_annotation_path Source code
get_fastq_files Source code
get_intergenic_ids Source code
get_intergenic_release_path Source code
get_kallisto_dir_path Source code
get_kallisto_program_path Source code
get_merged_fastq_file_names Source code
get_os Source code
get_output_dir Source code
get_ref_intergenic_ids Source code
get_species_path Source code
get_tool_output_path Source code
get_tool_path Source code
get_tool_transcriptome_path Source code
get_transcriptome_path Source code
init_userMetadata_from_dataframe Source code
intergenic_tx2gene Source code
is_kallisto_installed Source code
is_pair_end Source code
listIntergenicReleases Source code
list_bgee_ref_intergenic_species Man page Source code
list_community_ref_intergenic_species Man page Source code
list_intergenic_release Man page Source code
load_gene_to_biotype Source code
load_transcript_to_biotype Source code
merge_transcriptome_and_intergenic Man page Source code
plot_distributions Source code
quiet Source code
removeTxVersionFromAbundance Source code
retrieve_community_ref_intergenic_url Source code
retrieve_intergenic_path Source code
run_from_dataframe Source code
run_from_file Source code
run_from_object Source code
run_kallisto Man page Source code
run_tximport Man page Source code
setAnnotationFromFile Man page
setAnnotationFromFile,UserMetadata,character,character-method Man page
setAnnotationFromFile,UserMetadata,character,missing-method Man page
setAnnotationFromFile,userMetadata,character,character Man page
setAnnotationFromObject Man page
setAnnotationFromObject,UserMetadata,GRanges,character-method Man page
setAnnotationFromObject,userMetadata,GRanges,character Man page
setIntergenicRelease Man page
setIntergenicRelease,BgeeMetadata,character-method Man page
setIntergenicRelease,bgeeMetadata,character Man page
setOutputDir Man page
setOutputDir,UserMetadata,character-method Man page
setOutputDir,userMetadata,character Man page
setRNASeqLibPath Man page
setRNASeqLibPath,UserMetadata,character-method Man page
setRNASeqLibPath,userMetadata,character Man page
setRunIds Man page
setRunIds,UserMetadata,character-method Man page
setRunIds,userMetadata,character Man page
setSimpleArborescence Man page
setSimpleArborescence,UserMetadata,logical-method Man page
setSimpleArborescence,userMetadata,logical Man page
setTranscriptomeFromFile Man page
setTranscriptomeFromFile,UserMetadata,character,character-method Man page
setTranscriptomeFromFile,UserMetadata,character,missing-method Man page
setTranscriptomeFromFile,userMetadata,character,character Man page
setTranscriptomeFromFile,userMetadata,character,missing Man page
setTranscriptomeFromObject Man page
setTranscriptomeFromObject,UserMetadata,DNAStringSet,character-m Man page
setTranscriptomeFromObject,userMetadata,DNAStringSet,character Man page
setWorkingPath Man page
setWorkingPath,UserMetadata,character-method Man page
setWorkingPath,userMetadata,character Man page
transform_tximport Source code
BgeeCall documentation built on Dec. 12, 2020, 2 a.m.

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