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>

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

Installation

To install this package, start R (version "3.6") 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")

Vignette Title HTML R Script

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpressionWorkflow, Workflow

Version 1.0.1

In Bioconductor since BioC 3.11 (R-4.0) (4 years)

License GPL-3

Depends R (>= 3.6.0)

Imports GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer, BgeeDB, biomaRt, methods, grDevices, graphics, stats, utils

System Requirements kallisto

URL https://github.com/BgeeDB/BgeeCall

Bug Reports https://github.com/BgeeDB/BgeeCall/issues

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_1.0.1.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 git@git.bioconductor.org:packages/BgeeCall

Package Short Url https://bioconductor.org/packages/BgeeCall/

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