BgeeCall

DOI: 10.18129/B9.bioc.BgeeCall    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BgeeCall.

BgeeCall, a R package for automatic RNA-Seq present/absent gene expression calls generation

Bioconductor version: 3.9

Reference intergenic regions are generated by the Bgee RNA-Seq pipeliene. These intergenic regions are used to generate all Bgee RNA-Seq present/absent expression calls. This package now allows to generate your own present/absent calls using both these intergenic regions and the expertise of Bgee, as long as your species is present in Bgee. The threshold of present/absent expression is no longer arbitrary defined but is calculated based on expression of all RNA-Seq libraries integrated in Bgee.

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>

Installation

To install this package, start R (version "3.6") 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	Vignette Title
Text		NEWS

Details

biocViews	GeneExpressionWorkflow, Workflow
Version	1.0.1
License	GPL-3
Depends	R (>= 3.6.0)
Imports	GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer, BgeeDB, biomaRt, 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

Package Archives

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

Source Package	BgeeCall_1.0.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/BgeeCall
Source Repository (Developer Access)	git clone [email protected]:packages/BgeeCall
Package Short Url	https://bioconductor.org/packages/BgeeCall/
Package Downloads Report	Download Stats