DOI: 10.18129/B9.bioc.BgeeCall    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BgeeCall.

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

Bioconductor version: 3.9

Reference intergenic regions are generated by the Bgee RNA-Seq pipeliene. These intergenic regions are used to generate all Bgee RNA-Seq present/absent expression calls. This package now allows to generate your own present/absent calls using both these intergenic regions and the expertise of Bgee, as long as your species is present in Bgee. 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 [aut, cre], Julien Roux [aut], Sara Fonseca Costa [ctb], Marc Robinson Rechavi [ctb], Frederic Bastian [aut]

Maintainer: Julien Wollbrett <julien.wollbrett at>

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biocViews GeneExpressionWorkflow, Workflow
Version 1.0.1
License GPL-3
Depends R (>= 3.6.0)
Imports GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer, BgeeDB, biomaRt, methods, grDevices, graphics, stats, utils
Suggests knitr, testthat, rmarkdown, AnnotationHub, httr
SystemRequirements kallisto
Depends On Me
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