bumphunter
Bump Hunter
Bioconductor version: Release (3.19)
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 "4.4") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Epigenetics, ImmunoOncology, Infrastructure, MultipleComparison, Software |
| Version | 1.46.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11.5 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 | DAMEfinder, coMethDMR, derfinder, dmrseq, epimutacions, epivizr, methylCC, rnaEditr, 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.
| Source Package | bumphunter_1.46.0.tar.gz |
| Windows Binary (x86_64) | bumphunter_1.46.0.zip (64-bit only) |
| macOS Binary (x86_64) | bumphunter_1.46.0.tgz |
| macOS Binary (arm64) | bumphunter_1.46.0.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 |