branchpointer specifications

Information


Unique identifier OMICS_16653
Name branchpointer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.7.0
Stability Stable
Requirements
stats, plyr, parallel, IRanges, GenomicRanges, utils, S4Vectors, GenomeInfoDb, Biostrings, rtracklayer, BiocStyle, ggplot2, biomaRt, data.table, knitr, stringr, R(>=3.4), caret, cowplot, kernlab, gbm, BSgenome.Hsapiens.UCSC.hg38
Maintained Yes

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Maintainers


  • person_outline Beth Signal <>
  • person_outline Marcel Dinger <>

Publication for branchpointer

branchpointer in publication

PMCID: 5905632
PMID: 29155928
DOI: 10.1093/bioinformatics/btx727

[…] exact code changes can be tracked in our forked repository (https://i12g-gagneurweb.informatik.tu-muenchen.de/gitlab/avsec/splice_branchpoints). , all the models use the same set of features as ., branchpointer: branchpoint prediction model developed by . it is a combination of two stacked models: support vector machine (svm) with ‘rbfdot’ kernel and a gradient-boosted decision trees model, […]


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branchpointer institution(s)
Garvan Institute of Medical Research, Sydney, Australia; St Vincent’s Clinical School, University of New South Wales, Sydney, Australia
branchpointer funding source(s)
Paramor Family Philanthropic funding and Australian National Health and Medical Research Council (NHMRC) Australia Fellowship (1062470); an Australian Postgraduate Award; a Cancer Institute NSW Early Career Fellowship 13/ECF/1-45 and the Kinghorn Foundation.

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