bumphunter

DOI: 10.18129/B9.bioc.bumphunter    

Bump Hunter

Bioconductor version: Release (3.7)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("bumphunter")

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, Infrastructure, MultipleComparison, Software
Version 1.22.0
In Bioconductor since BioC 2.12 (R-3.0) (5.5 years)
License Artistic-2.0
Depends R (>= 3.4), 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/ririzarr/bumphunter
Depends On Me minfi
Imports Me ChAMP, derfinder, dmrseq, methyvim, recountWorkflow
Suggests Me derfinderPlot, epivizrData, regionReport
Links To Me
Build Report  

Package Archives

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

Source Package bumphunter_1.22.0.tar.gz
Windows Binary bumphunter_1.22.0.zip
Mac OS X 10.11 (El Capitan) bumphunter_1.22.0.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 http://bioconductor.org/packages/bumphunter/
Package Downloads Report Download Stats

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