factR

DOI: 10.18129/B9.bioc.factR    

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

Functional Annotation of Custom Transcriptomes

Bioconductor version: Development (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>

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

Installation

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

 

HTML R Script factR
PDF   Reference Manual

Details

biocViews AlternativeSplicing, FunctionalPrediction, GenePrediction, Software
Version 0.99.7
In Bioconductor since BioC 3.16 (R-4.2)
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)
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_0.99.7.tar.gz
Windows Binary factR_0.99.7.zip (64-bit only)
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/factR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/factR
Package Short Url https://bioconductor.org/packages/factR/
Package Downloads Report Download Stats

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