bumphunter

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see bumphunter.

Bump Hunter


Bioconductor version: 3.11

Tools for finding bumps in genomic data

Author: Rafael A. Irizarry [cre, 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]

Maintainer: Rafael A. Irizarry <rafa at jimmy.harvard.edu>

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

Installation

To install this package, start R (version "4.0") and enter:


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

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")
The bumphunter user's guide PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, Epigenetics, ImmunoOncology, Infrastructure, MultipleComparison, Software
Version 1.30.0
In Bioconductor since BioC 2.12 (R-3.0) (11 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/ririzarr/bumphunter
See More
Suggests testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
Linking To
Enhances
Depends On Me minfi
Imports Me brainflowprobes, ChAMP, DAMEfinder, derfinder, dmrseq, epivizr, GenomicState, methylCC, methyvim, 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.

Source Package bumphunter_1.30.0.tar.gz
Windows Binary bumphunter_1.30.0.zip
macOS 10.13 (High Sierra) bumphunter_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/bumphunter
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bumphunter
Bioc Package Browser https://code.bioconductor.org/browse/bumphunter/
Package Short Url https://bioconductor.org/packages/bumphunter/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive