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 unil.ch>
citation("BgeeCall")):
Installation
To install this package, start R (version "3.6") 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")| Vignette Title | HTML | R Script |
| NEWS | Text |
Details
| biocViews | GeneExpressionWorkflow, Workflow |
| Version | 1.0.1 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | GPL-3 |
| Depends | R (>= 3.6.0) |
| Imports | GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer, BgeeDB, biomaRt, methods, grDevices, graphics, stats, utils |
| System Requirements | kallisto |
| URL | https://github.com/BgeeDB/BgeeCall |
| Bug Reports | https://github.com/BgeeDB/BgeeCall/issues |
See More
| 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_1.0.1.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | |
| Source Repository | git clone https://git.bioconductor.org/packages/BgeeCall |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BgeeCall |
| Package Short Url | https://bioconductor.org/packages/BgeeCall/ |
| Package Downloads Report | Download Stats |