factR

This is the released version of factR; for the devel version, see factR.

Functional Annotation of Custom Transcriptomes

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DOI: 10.18129/B9.bioc.factR

Bioconductor version: Release (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")
BiocManager::install("factR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AlternativeSplicing, FunctionalPrediction, GenePrediction, Software

Version 1.11.0

In Bioconductor since BioC 3.16 (R-4.2) (3 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/