factR

DOI: 10.18129/B9.bioc.factR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see factR.

Functional Annotation of Custom Transcriptomes

Bioconductor version: 3.16

factR contain tools to process and interact with custom-assembled transcriptomes (GTF). At its core, factR constructs CDS information on custom transcripts and subsequently predicts its functional output. In addition, factR has tools capable of plotting transcripts, correcting chromosome and gene information and shortlisting new transcripts.

Author: Fursham Hamid [aut, cre]

Maintainer: Fursham Hamid <fursham.h at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("factR")

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("factR")

 

HTML	R Script	factR
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	AlternativeSplicing, FunctionalPrediction, GenePrediction, Software
Version	1.0.0
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	file LICENSE
Depends	R (>= 4.2)
Imports	BiocGenerics(>= 0.38), Biostrings(>= 2.60), GenomeInfoDb(>= 1.28), dplyr (>= 1.0), GenomicFeatures(>= 1.44), GenomicRanges(>= 1.44), IRanges(>= 2.26), purrr (>= 0.3), rtracklayer(>= 1.52), tidyr (>= 1.1), methods (>= 4.0), BiocParallel(>= 1.26), S4Vectors(>= 0.30), data.table (>= 1.14), rlang (>= 1.0), tibble (>= 3.1), wiggleplotr(>= 1.16), RCurl (>= 1.98), XML (>= 3.99), drawProteins(>= 1.12), ggplot2 (>= 3.3), stringr (>= 1.4), pbapply (>= 1.5), stats (>= 4.1), utils (>= 4.1), graphics (>= 4.1), crayon
LinkingTo
Suggests	AnnotationHub(>= 2.22), BSgenome(>= 1.58), BSgenome.Mmusculus.UCSC.mm10, testthat, knitr, rmarkdown, markdown, zeallot, rmdformats, bio3d (>= 2.4), signalHsmm (>= 1.5), tidyverse (>= 1.3), covr, patchwork
SystemRequirements
Enhances
URL	https://fursham-h.github.io/factR/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	factR_1.0.0.tar.gz
Windows Binary	factR_1.0.0.zip
macOS Binary (x86_64)	factR_1.0.0.tgz
macOS Binary (arm64)	factR_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/factR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/factR
Bioc Package Browser	https://code.bioconductor.org/browse/factR/
Package Short Url	https://bioconductor.org/packages/factR/
Package Downloads Report	Download Stats