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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 (3.19)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews GeneExpression, RNASeq, Software
Version 1.19.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
System Requirements kallisto
URL https://github.com/BgeeDB/BgeeCall
Bug Reports https://github.com/BgeeDB/BgeeCall/issues
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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_1.19.0.tar.gz
Windows Binary BgeeCall_1.19.0.zip
macOS Binary (x86_64) BgeeCall_1.19.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/BgeeCall
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BgeeCall
Bioc Package Browser https://code.bioconductor.org/browse/BgeeCall/
Package Short Url https://bioconductor.org/packages/BgeeCall/
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