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Bioconductor - BgeeCall (development version)

BgeeCall

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

Automatic RNA-Seq present/absent gene expression calls generation

Bioconductor version: Development (3.22)

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>

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

To install this package, start R (version "4.5") and enter:


if (!require("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

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 Details biocViews GeneExpression, RNASeq, Software Version 1.25.0 In Bioconductor since BioC 3.11 (R-4.0) (5 years) License GPL-3 + file LICENSE Depends R (>= 3.6) Imports GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5, txdbmaker System Requirements kallisto URL https://github.com/BgeeDB/BgeeCall Bug Reports https://github.com/BgeeDB/BgeeCall/issues See More Package Archives

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

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