BgeeCall

DOI: 10.18129/B9.bioc.BgeeCall    

Automatic RNA-Seq present/absent gene expression calls generation

Bioconductor version: Release (3.11)

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], Julien Roux [aut], Sara Fonseca Costa [ctb], 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 "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script automatic RNA-Seq present/absent gene expression calls generation
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, RNASeq, Software
Version 1.4.1
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
License GPL-3
Depends R (>= 3.6)
Imports GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer, biomaRt, jsonlite, methods, grDevices, graphics, stats, utils
LinkingTo
Suggests knitr, testthat, rmarkdown, AnnotationHub, httr
SystemRequirements kallisto
Enhances
URL https://github.com/BgeeDB/BgeeCall
BugReports https://github.com/BgeeDB/BgeeCall/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package BgeeCall_1.4.1.tar.gz
Windows Binary BgeeCall_1.4.1.zip
macOS 10.13 (High Sierra) BgeeCall_1.4.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/BgeeCall
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BgeeCall
Package Short Url https://bioconductor.org/packages/BgeeCall/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive

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