BgeeCall

DOI: 10.18129/B9.bioc.BgeeCall    

This is the development version of BgeeCall; for the stable release version, see BgeeCall.

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

Bioconductor version: Development (3.11)

Reference intergenic regions are generated by the Bgee RNA-Seq pipeline. These intergenic regions are used to generate all Bgee RNA-Seq present/absent expression calls. BgeeCall now allows to generate present/absent calls for any RNA-Seq library as long as reference intergenic sequences have been generated for the corresponding species. 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 <julien.wollbrett at unil.ch>, Julien Roux <julien.wollbrett at unil.ch>, Sara Fonseca Costa <julien.wollbrett at unil.ch>, Marc Robinson Rechavi <julien.wollbrett at unil.ch>, Frederic Bastian <julien.wollbrett at unil.ch>

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

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("BgeeCall")

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

Documentation

Details

biocViews	GeneExpression, RNASeq, Software, Workflow
Version	1.3.0
License	GPL-3
Depends	R (>= 3.6.0)
Imports	GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer, BgeeDB, 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
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Package Archives

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

Source Package
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 git@git.bioconductor.org:packages/BgeeCall
Package Short Url	https://bioconductor.org/packages/BgeeCall/
Package Downloads Report	Download Stats