bumphunter: Bump Hunter

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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]
Date of publication
None
Maintainer
Rafael A. Irizarry <rafa@jimmy.harvard.edu>
License
Artistic-2.0
Version
1.14.0
URLs

View on Bioconductor

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

Files in this package

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