BgeeCall

Automatic RNA-Seq present/absent gene expression calls generation


Bioconductor version: Release (3.19)

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).

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

Maintainer: Julien Wollbrett <julien.wollbrett at unil.ch>

Citation (from within R, enter citation("BgeeCall")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BgeeCall")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BgeeCall")
automatic RNA-Seq present/absent gene expression calls generation HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, RNASeq, Software
Version 1.20.1
In Bioconductor since BioC 3.11 (R-4.0) (4.5 years)
License GPL-3 + file LICENSE
Depends R (>= 3.6)
Imports GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5, txdbmaker
System Requirements kallisto
URL https://github.com/BgeeDB/BgeeCall
Bug Reports https://github.com/BgeeDB/BgeeCall/issues
See More
Suggests knitr, testthat, rmarkdown, AnnotationHub, httr
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BgeeCall_1.20.1.tar.gz
Windows Binary (x86_64) BgeeCall_1.20.1.zip
macOS Binary (x86_64) BgeeCall_1.20.1.tgz
macOS Binary (arm64) BgeeCall_1.20.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/BgeeCall
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BgeeCall
Bioc Package Browser https://code.bioconductor.org/browse/BgeeCall/
Package Short Url https://bioconductor.org/packages/BgeeCall/
Package Downloads Report Download Stats