BgeeCall

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see BgeeCall.

Automatic RNA-Seq present/absent gene expression calls generation

Bioconductor version: 3.13

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 "4.1") 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")

automatic RNA-Seq present/absent gene expression calls generation HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, RNASeq, Software

Version 1.8.0

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

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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