normr: Normalization and difference calling in ChIP-seq data
Version 1.2.0

Robust normalization and difference calling procedures for ChIP-seq and alike data. Read counts are modeled jointly as a binomial mixture model with a user-specified number of components. A fitted background estimate accounts for the effect of enrichment in certain regions and, therefore, represents an appropriate null hypothesis. This robust background is used to identify significantly enriched or depleted regions.

AuthorJohannes Helmuth [aut, cre], Ho-Ryun Chung [aut]
Bioconductor views Alignment Bayesian ChIPSeq Classification DataImport DifferentialPeakCalling FunctionalGenomics Genetics MultipleComparison Normalization PeakDetection Preprocessing RIPSeq
Date of publicationNone
MaintainerJohannes Helmuth <helmuth@molgen.mpg.de>
LicenseGPL-2
Version1.2.0
URL https://github.com/your-highness/normR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("normr")

Getting started

README.md
Introduction to the normR package

Popular man pages

normR: Enrichment, Difference and Regime Calling in ChIP-seq data.
NormRCountConfig-class: Container for configuration of read counting with bamsignals...
normR-diffR: Difference Calling between conditional ChIP-seq data in normR...
normR-enrichR: Enrichment Calling on ChIP-seq data in normR with enrichR
NormRFit-class: Container for a fit done with normR
normR-regimeR: Regime Enrichment Calling for ChIP-seq data in normR with...
See all...

All man pages Function index File listing

Man pages

normR: Enrichment, Difference and Regime Calling in ChIP-seq data.
NormRCountConfig-class: Container for configuration of read counting with bamsignals...
normR-diffR: Difference Calling between conditional ChIP-seq data in normR...
normR-enrichR: Enrichment Calling on ChIP-seq data in normR with enrichR
NormRFit-class: Container for a fit done with normR
normR-regimeR: Regime Enrichment Calling for ChIP-seq data in normR with...

Functions

BamsignalsConfig Man page
BamsignalsCountConfig Man page
DifferenceCalling Man page
DifferentialPeakCalling Man page
EnrichmentCalling Man page
NormRCountConfig Man page
NormRCountConfig-class Man page
NormRFit Man page
NormRFit-class Man page
NormRfit Man page
PeakCalling Man page
RegimeCalling Man page
computeEnrichmentWithMap Source code
configPairedEnd Man page
configSingleEnd Man page
countConfigPairedEnd Man page
countConfigPairedEnd,ANY-method Man page
countConfigSingleEnd Man page
countConfigSingleEnd,ANY-method Man page
diffR Man page
diffR,character,character,GenomicRanges-method Man page
diffR,character,character,character-method Man page
diffR,character,character,data.frame-method Man page
diffR,integer,integer,GenomicRanges-method Man page
diffR-generic Man page
differenceCall Man page
diffr Man page
em Source code
enrichR Man page
enrichR,character,character,GenomicRanges-method Man page
enrichR,character,character,character-method Man page
enrichR,character,character,data.frame-method Man page
enrichR,integer,integer,GenomicRanges-method Man page
enrichR-generic Man page
enrichmentCall Man page
enrichr Man page
exportR Man page
exportR,NormRFit,character-method Man page
getBamsignalsFilter Man page
getClasses Man page
getClasses,NormRFit-method Man page
getCounts Man page
getCounts,NormRFit-method Man page
getEnrichment Man page
getEnrichment,NormRFit-method Man page
getFilter Man page
getFilter,NormRCountConfig-method Man page
getNormRCountConfigFilter Man page
getPosteriors Man page
getPosteriors,NormRFit-method Man page
getPvalues Man page
getPvalues,NormRFit-method Man page
getQvalues Man page
getQvalues,NormRFit-method Man page
getRanges Man page
getRanges,NormRFit-method Man page
handleCharCharChar Source code
handleCharCharDf Source code
handleCharCharGR Source code
length,NormRFit-method Man page
logRowSum Source code
logSumVector Source code
mapToOriginal Source code
mapToUniqueWithMap Source code
normR Man page
normR-package Man page
normRFit Man page
normr Man page
normr_core Source code
normrfit Man page
plot,NormRFit,missing-method Man page
plot.NormRFit Man page
print,NormRCountConfig-method Man page
print,NormRFit-method Man page
regimeCall Man page
regimeR Man page
regimeR,character,character,GenomicRanges,numeric-method Man page
regimeR,character,character,character,numeric-method Man page
regimeR,character,character,data.frame,numeric-method Man page
regimeR,integer,integer,GenomicRanges,numeric-method Man page
regimeR-generic Man page
regimer Man page
show,NormRCountConfig-method Man page
show,NormRFit-method Man page
summary,NormRFit-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/NormRCountConfig.R
R/NormRFit.R
R/RcppExports.R
R/methods.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/normr.R
inst/doc/normr.Rmd
inst/doc/normr.html
inst/examples
inst/examples/NormRCountConfig_example.R
inst/examples/NormRFit_example.R
inst/examples/methods_example.R
inst/extdata
inst/extdata/1a.png
inst/extdata/1b.png
inst/extdata/2.png
inst/extdata/3.png
inst/extdata/K562_H3K36me3.bam
inst/extdata/K562_H3K36me3.bam.bai
inst/extdata/K562_H3K4me3.bam
inst/extdata/K562_H3K4me3.bam.bai
inst/extdata/K562_Input.bam
inst/extdata/K562_Input.bam.bai
inst/extdata/bamgeneration
inst/extdata/genes.bed
inst/extdata/header.sam
man
man/NormRCountConfig-class.Rd
man/NormRFit-class.Rd
man/normR-diffR.Rd
man/normR-enrichR.Rd
man/normR-regimeR.Rd
man/normR.Rd
src
src/Makevars
src/RcppExports.cpp
src/em.cpp
src/normr_init.c
tests
tests/testthat
tests/testthat.R
tests/testthat/test-CLI.R
tests/testthat/test-NormRFit.R
tests/testthat/test-methods.R
tests/testthat/utils.R
vignettes
vignettes/normr.Rmd
normr documentation built on May 20, 2017, 10:32 p.m.

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