This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see BgeeCall.
Bioconductor version: 3.10
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 [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 (from within R,
enter citation("BgeeCall")
):
To install this package, start R (version "3.6") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BgeeCall")
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:
browseVignettes("BgeeCall")
HTML | R Script | automatic RNA-Seq present/absent gene expression calls generation |
Text | NEWS |
biocViews | GeneExpression, RNASeq, Software, Workflow |
Version | 1.2.1 |
In Bioconductor since | BioC 3.11 (R-4.0) (< 6 months) |
License | GPL-3 |
Depends | R (>= 3.6.0) |
Imports | GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer, biomaRt, jsonlite, methods, grDevices, graphics, stats, utils |
LinkingTo | |
Suggests | knitr, testthat, rmarkdown, AnnotationHub, httr |
SystemRequirements | kallisto |
Enhances | |
URL | https://github.com/BgeeDB/BgeeCall |
BugReports | https://github.com/BgeeDB/BgeeCall/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me |
Follow Installation instructions to use this package in your R session.
Source Package | BgeeCall_1.2.1.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 |
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