branchpointer
Prediction of intronic splicing branchpoints
Bioconductor version: 3.24 · Package version: 1.39.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("branchpointer")Details
| Maintainer | Beth Signal <b.signal@garvan.org.au> |
| Author | Beth Signal |
| License | BSD_3_clause + file LICENSE |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GenomeAnnotation, GenomicVariation, MotifAnnotation, Software |
| Package Short Url | https://bioconductor.org/packages/branchpointer/ |
Citation
From within R, enter citation("branchpointer"):
Beth Signal. branchpointer: Prediction of intronic splicing branchpoints. doi:10.18129/B9.bioc.branchpointer, R package version 1.39.0, https://bioconductor.org/packages/branchpointer.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | branchpointer_1.39.0.tar.gz |
| Windows binary (x86_64) | branchpointer_1.39.0.zip |
| macOS binary (arm64) | branchpointer_1.39.0.tgz |
| macOS binary (x86_64) | branchpointer_1.39.0.tgz |
Dependencies
Depends: caret, R (>= 3.4)
Imports: plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, Seqinfo, IRanges, S4Vectors, data.table