DOI: 10.18129/B9.bioc.BgeeCall    

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

BgeeCall, a R package for automatic RNA-Seq present/absent gene expression calls generation

Bioconductor version: Development (3.11)

Reference intergenic regions are generated by the Bgee RNA-Seq pipeline. These intergenic regions are used to generate all Bgee RNA-Seq present/absent expression calls. BgeeCall now allows to generate present/absent calls for any RNA-Seq library as long as reference intergenic sequences have been generated for the corresponding species. The threshold of present/absent expression is no longer arbitrary defined but is calculated based on expression of all RNA-Seq libraries integrated in Bgee.

Author: Julien Wollbrett <julien.wollbrett at>, Julien Roux <julien.wollbrett at>, Sara Fonseca Costa <julien.wollbrett at>, Marc Robinson Rechavi <julien.wollbrett at>, Frederic Bastian <julien.wollbrett at>

Maintainer: Julien Wollbrett <julien.wollbrett at>

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


To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel


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



biocViews GeneExpression, RNASeq, Software, Workflow
Version 1.3.0
License GPL-3
Depends R (>= 3.6.0)
Imports GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer, BgeeDB, biomaRt, jsonlite, methods, grDevices, graphics, stats, utils
Suggests knitr, testthat, rmarkdown, AnnotationHub, httr
SystemRequirements kallisto
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

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

Source Package
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: