normr: Normalization and difference calling in ChIP-seq data

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]
Date of publicationNone
MaintainerJohannes Helmuth <helmuth@molgen.mpg.de>
LicenseGPL-2
Version1.0.0
https://github.com/your-highness/normR

View on Bioconductor

Functions

BamsignalsConfig Man page
BamsignalsCountConfig Man page
configPairedEnd Man page
configSingleEnd Man page
countConfigPairedEnd Man page
countConfigPairedEnd,ANY-method Man page
countConfigSingleEnd Man page
countConfigSingleEnd,ANY-method Man page
differenceCall Man page
DifferenceCalling Man page
DifferentialPeakCalling Man page
diffr Man page
diffR Man page
diffR,character,character,character-method Man page
diffR,character,character,data.frame-method Man page
diffR,character,character,GenomicRanges-method Man page
diffR-generic Man page
diffR,integer,integer,GenomicRanges-method Man page
enrichmentCall Man page
EnrichmentCalling Man page
enrichr Man page
enrichR Man page
enrichR,character,character,character-method Man page
enrichR,character,character,data.frame-method Man page
enrichR,character,character,GenomicRanges-method Man page
enrichR-generic Man page
enrichR,integer,integer,GenomicRanges-method 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
length,NormRFit-method Man page
normr Man page
normR Man page
NormRCountConfig Man page
NormRCountConfig-class Man page
normrfit Man page
normRFit Man page
NormRfit Man page
NormRFit Man page
NormRFit-class Man page
normR-package Man page
PeakCalling Man page
plot.NormRFit Man page
plot,NormRFit,missing-method Man page
print,NormRCountConfig-method Man page
print,NormRFit-method Man page
regimeCall Man page
RegimeCalling Man page
regimer Man page
regimeR Man page
regimeR,character,character,character,numeric-method Man page
regimeR,character,character,data.frame,numeric-method Man page
regimeR,character,character,GenomicRanges,numeric-method Man page
regimeR-generic Man page
regimeR,integer,integer,GenomicRanges,numeric-method Man page
show,NormRCountConfig-method Man page
show,NormRFit-method Man page
summary,NormRFit-method Man page

Files

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

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

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

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