BgeeCall
Automatic RNA-Seq present/absent gene expression calls generation
Bioconductor version: 3.23 · Package version: 1.28.4
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BgeeCall")Details
| Maintainer | Julien Wollbrett <julien.wollbrett@unil.ch> |
| Author | Julien Wollbrett [aut, cre], Alessandro Brandulas Cammarata [aut], Sara Fonseca Costa [aut], Julien Roux [aut], Marc Robinson Rechavi [ctb], Frederic Bastian [aut] |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/BgeeDB/BgeeCall |
| Bug Reports | https://github.com/BgeeDB/BgeeCall/issues |
| System Requirements | kallisto |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, RNASeq, Software |
| Package Short Url | https://bioconductor.org/packages/BgeeCall/ |
Citation
From within R, enter citation("BgeeCall"):
Julien Wollbrett, Alessandro Brandulas Cammarata, Sara Fonseca Costa, Julien Roux, Frederic Bastian. BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation. doi:10.18129/B9.bioc.BgeeCall, R package version 1.28.4, https://bioconductor.org/packages/BgeeCall.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | BgeeCall_1.28.4.tar.gz |
| Windows binary (x86_64) | BgeeCall_1.28.4.zip |
| macOS binary (arm64) | BgeeCall_1.28.4.tgz |
| macOS binary (x86_64) | BgeeCall_1.28.4.tgz |
Dependencies
Depends: R (>= 3.6)
Imports: AnnotationDbi, curl, ggplot2, scales, GenomicFeatures, tximport, Biostrings, readr, sjmisc, RCurl, RSQLite, tools, stringr, rtracklayer, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5, txdbmaker, IRanges, spatstat.univar
Suggests: knitr, testthat, rmarkdown, AnnotationHub, GenomeInfoDb, httr