BgeeCall

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

Automatic RNA-Seq present/absent gene expression calls generation

Bioconductor version: Development (3.24)

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], Alessandro Brandulas Cammarata [aut], Sara Fonseca Costa [aut], Julien Roux [aut], Marc Robinson Rechavi [ctb], Frederic Bastian [aut]

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

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

Julien Wollbrett, Alessandro Brandulas Cammarata, Sara Fonseca Costa, Julien Roux, Frederic Bastian. BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation. doi:10.18129/B9.bioc.BgeeCall, R package version 1.29.3, https://bioconductor.org/packages/BgeeCall.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, RNASeq, Software
Version	1.29.3
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 3.6)
Imports	AnnotationDbi, curl, ggplot2, scales, GenomicFeatures, tximport, Biostrings, readr, sjmisc, RCurl, RSQLite, tools, stringr, rtracklayer, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5, txdbmaker, IRanges, spatstat.univar
System Requirements	kallisto
URL	https://github.com/BgeeDB/BgeeCall
Bug Reports	https://github.com/BgeeDB/BgeeCall/issues

Suggests	knitr, testthat, rmarkdown, AnnotationHub, GenomeInfoDb, httr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	BgeeCall_1.29.3.tar.gz
Windows Binary (x86_64)	BgeeCall_1.29.3.zip
macOS Binary (big-sur-x86_64)	BgeeCall_1.29.3.tgz
macOS Binary (sonoma-arm64)	BgeeCall_1.29.3.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