BgeeCall

Automatic RNA-Seq present/absent gene expression calls generation

Bioconductor version: 3.23 · Package version: 1.28.4

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).

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BgeeCall")

Details

Maintainer	Julien Wollbrett <julien.wollbrett@unil.ch>
Author	Julien Wollbrett [aut, cre], Alessandro Brandulas Cammarata [aut], Sara Fonseca Costa [aut], Julien Roux [aut], Marc Robinson Rechavi [ctb], Frederic Bastian [aut]
License	GPL-3 + file LICENSE
URL	https://github.com/BgeeDB/BgeeCall
Bug Reports	https://github.com/BgeeDB/BgeeCall/issues
System Requirements	kallisto
Downloads rank	324
Source branch	RELEASE_3_23
biocViews	GeneExpression, RNASeq, Software

Documentation

automatic RNA-Seq present/absent gene expression calls generation

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Source package

Dependencies

Depends: R (>= 3.6)

Imports: AnnotationDbi, curl, ggplot2, scales, GenomicFeatures, tximport, Biostrings, readr, sjmisc, RCurl, RSQLite, tools, stringr, rtracklayer, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5, txdbmaker, IRanges, spatstat.univar

Suggests: knitr, testthat, rmarkdown, AnnotationHub, GenomeInfoDb, httr