Package: BgeeCall 1.23.0

Julien Wollbrett

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

BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (https://bgee.org).

Authors:Julien Wollbrett [aut, cre], Sara Fonseca Costa [aut], Julien Roux [aut], Marc Robinson Rechavi [ctb], Frederic Bastian [aut]

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BgeeCall.pdf |BgeeCall.html✨
BgeeCall/json (API)
NEWS

# Install 'BgeeCall' in R:

install.packages('BgeeCall', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bgeedb/bgeecall/issues

On BioConductor:BgeeCall-1.23.0(bioc 3.21)BgeeCall-1.22.0(bioc 3.20)

software geneexpression rnaseq biology gene-expression gene-level intergenic-regions present-absent-calls rna-seq rna-seq-libraries scrna-seq

5.56 score 3 stars 9 scripts 185 downloads 30 exports 104 dependencies

Last updated 2 months agofrom:6e9ba9e4b0. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:create_kallisto_index download_fasta_intergenic download_kallisto generate_calls_workflow generate_presence_absence generate_slurm_calls generate_slurm_indexes get_summary_stats getIntergenicPrefix getIntergenicRelease getRunIds getSimpleArborescence getWorkingPath list_bgee_ref_intergenic_species list_community_ref_intergenic_species list_intergenic_release merge_transcriptome_and_intergenic merging_libraries run_kallisto run_tximport setAnnotationFromFile setAnnotationFromObject setIntergenicRelease setOutputDir setRNASeqLibPath setRunIds setSimpleArborescence setTranscriptomeFromFile setTranscriptomeFromObject setWorkingPath

Dependencies:abind AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cli codetools cpp11 crayon curl data.table datawizard DBI dbplyr DelayedArray digest dplyr fansi fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue hms httr httr2 insight IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png prettyunits progress purrr R6 rappdirs RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools rslurm RSQLite rtracklayer S4Arrays S4Vectors sjlabelled sjmisc snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker tximport UCSC.utils utf8 vctrs whisker withr XML xml2 XVector yaml zlibbioc

automatic RNA-Seq present/absent gene expression calls generation

Julien Wollbrett, Sara Fonseca Costa, Marc Robinson-Rechavi, Frederic Bastian

Rendered frombgeecall-manual.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-07-30
Started: 2019-02-01

Citation

Development and contributors

Readme and manuals

Help Manual

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