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("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
| Reference Manual |
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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| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |