factR
Functional Annotation of Custom Transcriptomes
Bioconductor version: 3.23 · Package version: 1.14.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("factR")Details
| Maintainer | Fursham Hamid <fursham.h@gmail.com> |
| Author | Fursham Hamid [aut, cre] |
| License | file LICENSE |
| URL | https://fursham-h.github.io/factR/ |
| Downloads rank | 199 |
| Source branch | RELEASE_3_23 |
| biocViews | AlternativeSplicing, FunctionalPrediction, GenePrediction, Software |
Documentation
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Dependencies
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)
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