BgeeCall
This is the development version of BgeeCall; for the stable release version, see BgeeCall.
Automatic RNA-Seq present/absent gene expression calls generation
Bioconductor version: Development (3.20)
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 (https://bgee.org).
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 unil.ch>
citation("BgeeCall")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")
automatic RNA-Seq present/absent gene expression calls generation | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | GeneExpression, RNASeq, Software |
Version | 1.21.2 |
In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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, txdbmaker |
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 |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | BgeeCall_1.21.2.tar.gz |
Windows Binary | BgeeCall_1.21.2.zip |
macOS Binary (x86_64) | BgeeCall_1.21.2.tgz |
macOS Binary (arm64) | BgeeCall_1.21.2.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/BgeeCall |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BgeeCall |
Bioc Package Browser | https://code.bioconductor.org/browse/BgeeCall/ |
Package Short Url | https://bioconductor.org/packages/BgeeCall/ |
Package Downloads Report | Download Stats |