BgeeCall
This is the released version of BgeeCall; for the devel version, see BgeeCall.
Automatic RNA-Seq present/absent gene expression calls generation
Bioconductor version: Release (3.23)
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], Alessandro Brandulas Cammarata [aut], Sara Fonseca Costa [aut], Julien Roux [aut], Marc Robinson Rechavi [ctb], Frederic Bastian [aut]
Maintainer: Julien Wollbrett <julien.wollbrett at unil.ch>
citation("BgeeCall")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| automatic RNA-Seq present/absent gene expression calls generation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, RNASeq, Software |
| Version | 1.28.4 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL-3 + file LICENSE |
| 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 |
| System Requirements | kallisto |
| URL | https://github.com/BgeeDB/BgeeCall |
| Bug Reports | https://github.com/BgeeDB/BgeeCall/issues |
See More
| Suggests | knitr, testthat, rmarkdown, AnnotationHub, GenomeInfoDb, 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_1.28.4.tar.gz |
| Windows Binary (x86_64) | BgeeCall_1.28.4.zip |
| macOS Binary (big-sur-x86_64) | BgeeCall_1.28.4.tgz |
| macOS Binary (sonoma-arm64) | BgeeCall_1.28.4.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 |
| Old Source Packages for BioC 3.23 | Source Archive |