BgeeCall

DOI: 10.18129/B9.bioc.BgeeCall    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see BgeeCall.

Automatic RNA-Seq present/absent gene expression calls generation

Bioconductor version: 3.14

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>

Installation

To install this package, start R (version "4.1") 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")

 

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

Details

biocViews	GeneExpression, RNASeq, Software
Version	1.10.0
In Bioconductor since	BioC 3.11 (R-4.0) (2 years)
License	GPL-3
Depends	R (>= 3.6)
Imports	GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5
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_1.10.0.tar.gz
Windows Binary	BgeeCall_1.10.0.zip
macOS 10.13 (High Sierra)	BgeeCall_1.10.0.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