normr: Normalization and difference calling in ChIP-seq data

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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.

Author
Johannes Helmuth [aut, cre], Ho-Ryun Chung [aut]
Date of publication
None
Maintainer
Johannes Helmuth <helmuth@molgen.mpg.de>
License
GPL-2
Version
1.0.0
URLs

View on Bioconductor

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...

Files in this package

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