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factR

This is the development version of factR; for the stable release version, see factR.

Functional Annotation of Custom Transcriptomes


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("factR")):

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("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")
factR HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews AlternativeSplicing, FunctionalPrediction, GenePrediction, Software
Version 1.5.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License file LICENSE
Depends R (>= 4.2)
Imports BiocGenerics(>= 0.46), Biostrings(>= 2.68), GenomeInfoDb(>= 1.36), dplyr (>= 1.1), GenomicFeatures(>= 1.52), GenomicRanges(>= 1.52), IRanges(>= 2.34), purrr (>= 1.0), rtracklayer(>= 1.60), tidyr (>= 1.3), methods (>= 4.3), BiocParallel(>= 1.34), S4Vectors(>= 0.38), data.table (>= 1.14), rlang (>= 1.1), tibble (>= 3.2), wiggleplotr(>= 1.24), RCurl (>= 1.98), XML (>= 3.99), drawProteins(>= 1.20), ggplot2 (>= 3.4), stringr (>= 1.5), pbapply (>= 1.7), stats (>= 4.3), utils (>= 4.3), graphics (>= 4.3), crayon (>= 1.5)
System Requirements
URL https://fursham-h.github.io/factR/
See More
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
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Package Archives

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

Source Package factR_1.5.0.tar.gz
Windows Binary factR_1.5.0.zip
macOS Binary (x86_64) factR_1.5.0.tgz
macOS Binary (arm64) factR_1.5.0.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