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Bioconductor - bumphunter (development version)

bumphunter

This is the development version of bumphunter; for the stable release version, see bumphunter.

Bump Hunter

Bioconductor version: Development (3.22)

Tools for finding bumps in genomic data

Author: Rafael A. Irizarry [aut], Martin Aryee [aut], Kasper Daniel Hansen [aut], Hector Corrada Bravo [aut], Shan Andrews [ctb], Andrew E. Jaffe [ctb], Harris Jaffee [ctb], Leonardo Collado-Torres [ctb], Tamilselvi Guharaj [cre]

Maintainer: Tamilselvi Guharaj <selvi at ds.dfci.harvard.edu>

Citation (from within R, enter citation("bumphunter")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("bumphunter")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("bumphunter")
Details biocViews DNAMethylation, Epigenetics, ImmunoOncology, Infrastructure, MultipleComparison, Software Version 1.51.0 In Bioconductor since BioC 2.12 (R-3.0) (12.5 years) License Artistic-2.0 Depends R (>= 3.5), S4Vectors(>= 0.9.25), IRanges(>= 2.3.23), GenomeInfoDb, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats System Requirements URL https://github.com/rafalab/bumphunter See More Suggests testthat, RUnit, doParallel, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene Linking To Enhances Depends On Me minfi Imports Me coMethDMR, DAMEfinder, derfinder, dmrseq, epimutacions, epivizr, methylCC, rnaEditr, vmrseq, GenomicState, recountWorkflow Suggests Me bigmelon, derfinderPlot, epivizrData, regionReport Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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