DOI: 10.18129/B9.bioc.factR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see factR.

Functional Annotation of Custom Transcriptomes

Bioconductor version: 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")):


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biocViews AlternativeSplicing, FunctionalPrediction, GenePrediction, Software
Version 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
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), crayon
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
URL https://fursham-h.github.io/factR/
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Source Package factR_1.0.0.tar.gz
Windows Binary factR_1.0.0.zip
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