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Automatic RNA-Seq present/absent gene expression calls generation

Bioconductor version: Release (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 (

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>

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


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

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


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


Reference Manual PDF


biocViews GeneExpression, RNASeq, Software
Version 1.20.0
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
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Suggests knitr, testthat, rmarkdown, AnnotationHub, httr
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Follow Installation instructions to use this package in your R session.

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macOS Binary (x86_64) BgeeCall_1.20.1.tgz
macOS Binary (arm64) BgeeCall_1.20.1.tgz
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