BgeeCall

DOI: 10.18129/B9.bioc.BgeeCall    

This is the development version of BgeeCall; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (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 labrary 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")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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Details

biocViews GeneExpressionWorkflow, Workflow
Version 1.1.1
License GPL-3
Depends R (>= 3.6.0)
Imports GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer, BgeeDB, 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

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BgeeCall_1.1.1.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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