factR
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see factR.
Functional Annotation of Custom Transcriptomes
Bioconductor version: 3.18
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("factR")):
Installation
To install this package, start R (version "4.3") 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")| factR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, FunctionalPrediction, GenePrediction, Software |
| Version | 1.4.0 |
| 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 |
| 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.
| Source Package | factR_1.4.0.tar.gz |
| Windows Binary | factR_1.4.0.zip |
| macOS Binary (x86_64) | factR_1.4.0.tgz |
| macOS Binary (arm64) | factR_1.4.0.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 |