bumphunter

DOI: 10.18129/B9.bioc.bumphunter    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see bumphunter.

Bump Hunter

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DNAMethylation, Epigenetics, ImmunoOncology, Infrastructure, MultipleComparison, Software
Version	1.34.0
In Bioconductor since	BioC 2.12 (R-3.0) (8.5 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
LinkingTo
Suggests	testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL	https://github.com/rafalab/bumphunter
Depends On Me	minfi
Imports Me	brainflowprobes, ChAMP, DAMEfinder, derfinder, dmrseq, epivizr, GenomicState, methylCC, recountWorkflow, rnaEditr
Suggests Me	bigmelon, derfinderPlot, epivizrData, regionReport
Links To Me
Build Report

Package Archives

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

Source Package	bumphunter_1.34.0.tar.gz
Windows Binary	bumphunter_1.34.0.zip
macOS 10.13 (High Sierra)	bumphunter_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/bumphunter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/bumphunter
Package Short Url	https://bioconductor.org/packages/bumphunter/
Package Downloads Report	Download Stats