bumphunter: Bump Hunter
Version 1.16.0

Tools for finding bumps in genomic data

AuthorRafael 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]
Bioconductor views DNAMethylation Epigenetics Infrastructure MultipleComparison
Date of publicationNone
MaintainerRafael A. Irizarry <rafa@jimmy.harvard.edu>
LicenseArtistic-2.0
Version1.16.0
URL https://github.com/ririzarr/bumphunter
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("bumphunter")

Getting started

README.md

Popular man pages

annotateNearest: Annotate the results of nearest
annotateTranscripts: Annotate transcripts
bumphunter: Bumphunter
clusterMaker: Make clusters of genomic locations based on distance
loessByCluster: Apply loess smoothing to values within each spatially-defined...
regionFinder: Find non-zero regions in vector
runmedByCluster: Apply running median smoothing to values within each...
See all...

All man pages Function index File listing

Man pages

annotateNearest: Annotate the results of nearest
annotateTranscripts: Annotate transcripts
bumphunter: Bumphunter
clusterMaker: Make clusters of genomic locations based on distance
dummyData: Generate dummy data for use with bumphunter functions
getSegments: Segment a vector into positive, zero, and negative regions
locfitByCluster: Apply local regression smoothing to values within each...
loessByCluster: Apply loess smoothing to values within each spatially-defined...
matchGenes: Find and annotate closest genes to genomic regions
regionFinder: Find non-zero regions in vector
runmedByCluster: Apply running median smoothing to values within each...
smoother: Smooth genomic profiles
TT: Example data

Functions

TT Man page
annotateNearest Man page Source code
annotateTranscripts Man page Source code
boundedClusterMaker Man page Source code
bumphunter Man page
bumphunter,matrix-method Man page
bumphunter-methods Man page
bumphunterEngine Man page Source code
closeSockets Source code
clusterMaker Man page Source code
dummyData Man page Source code
foreachCleanup Source code
getEstimate Source code
getModT Source code
getSegments Man page Source code
getSegments_old Source code
greaterOrEqual Source code
locfitByCluster Man page Source code
loessByCluster Man page Source code
matchGenes Man page Source code
print.bumps Man page Source code
reduceIt Source code
regionFinder Man page Source code
runmedByCluster Man page Source code
smoother Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllGenerics.R
R/bumphunter.R
R/dummyData.R
R/limmaForPermutations.R
R/matchGenes.R
R/regionFinder.R
R/smooth.R
R/utils.R
README.md
build
build/vignette.rds
data
data/TT.rda
data/datalist
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/bumphunter.R
inst/doc/bumphunter.Rnw
inst/doc/bumphunter.pdf
inst/testData
inst/testData/testData.R
inst/testData/testData.Rout
inst/unitTests
inst/unitTests/bumpsTest1.rda
inst/unitTests/bumpsTest2.rda
inst/unitTests/loessSmoothed.rda
inst/unitTests/runmedSmoothed.rda
inst/unitTests/test_bumphunter.R
inst/unitTests/test_smoothers.R
man
man/TT.Rd
man/annotateNearest.Rd
man/annotateTranscripts.Rd
man/bumphunter.Rd
man/clusterMaker.Rd
man/dummyData.Rd
man/getSegments.Rd
man/locfitByCluster.Rd
man/loessByCluster.Rd
man/matchGenes.Rd
man/regionFinder.Rd
man/runmedByCluster.Rd
man/smoother.Rd
tests
tests/runTests.R
tests/test-all.R
tests/testthat
tests/testthat/test_annotation.R
vignettes
vignettes/bumphunter.Rnw
vignettes/bumphunter.bib
bumphunter documentation built on May 20, 2017, 9:36 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.