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Bioconductor - factR (development version)

factR

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

Functional Annotation of Custom Transcriptomes

Bioconductor version: Development (3.22)

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 "4.5") 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")
Details biocViews AlternativeSplicing, FunctionalPrediction, GenePrediction, Software Version 1.11.0 In Bioconductor since BioC 3.16 (R-4.2) (2.5 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 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.

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