Package: normr 1.39.2

Johannes Helmuth

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.

Authors:Johannes Helmuth [aut, cre], Ho-Ryun Chung [aut]

normr_1.39.2.tar.gz
normr_1.39.2.zip(r-4.7)normr_1.39.2.zip(r-4.6)normr_1.39.2.zip(r-4.5)
normr_1.39.2.tgz(r-4.6-x86_64)normr_1.39.2.tgz(r-4.6-arm64)normr_1.39.2.tgz(r-4.5-x86_64)normr_1.39.2.tgz(r-4.5-arm64)
normr_1.39.2.tar.gz(r-4.7-arm64)normr_1.39.2.tar.gz(r-4.7-x86_64)normr_1.39.2.tar.gz(r-4.6-arm64)normr_1.39.2.tar.gz(r-4.6-x86_64)
normr_1.39.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
normr/json (API)
NEWS

# Install 'normr' in R:

install.packages('normr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/your-highness/normr/issues

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On BioConductor:normr-1.39.2(bioc 3.24)normr-1.38.1(bioc 3.23)

bayesian differentialpeakcalling classification dataimport chipseq ripseq functionalgenomics genetics multiplecomparison normalization peakdetection preprocessing alignment cpp openmp

6.12 score 11 stars 398 downloads 18 exports 74 dependencies

Last updated from:f2ac4d8bc9. Checks:12 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	210
linux-devel-arm64	WARNING	321
linux-devel-x86_64	WARNING	391
source / vignettes	OK	353
linux-release-arm64	WARNING	344
linux-release-x86_64	WARNING	379
macos-release-arm64	WARNING	242
macos-release-x86_64	WARNING	430
macos-oldrel-arm64	WARNING	236
macos-oldrel-x86_64	WARNING	533
windows-devel	WARNING	273
windows-release	WARNING	317
windows-oldrel	WARNING	347
wasm-release	OK	162

Exports:countConfigPairedEnd countConfigSingleEnd diffR enrichR exportR getClasses getCounts getEnrichment getFilter getPosteriors getPvalues getQvalues getRanges plot print regimeR show summary

Dependencies:abind askpass bamsignals BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops cigarillo cli codetools cpp11 crayon curl DelayedArray farver formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl plyr qvalue R6 RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys UCSC.utils vctrs viridisLite withr XML XVector yaml

Introduction to the normR package

Johannes Helmuth

Rendered fromnormr.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2020-04-14
Started: 2016-07-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Difference Calling between conditional ChIP-seq data in normR with diffR	differenceCall DifferenceCalling diffR diffr diffR,character,character,character-method diffR,character,character,data.frame-method diffR,character,character,GenomicRanges-method diffR,integer,integer,GenomicRanges-method diffR-generic
Enrichment Calling on ChIP-seq data in normR with enrichR	enrichmentCall EnrichmentCalling enrichR enrichr enrichR,character,character,character-method enrichR,character,character,data.frame-method enrichR,character,character,GenomicRanges-method enrichR,integer,integer,GenomicRanges-method enrichR-generic
Enrichment, Difference and Regime Calling in ChIP-seq data.	normR-package DifferentialPeakCalling normR normr PeakCalling
Container for configuration of read counting with bamsignals in normR	BamsignalsConfig BamsignalsCountConfig configPairedEnd configSingleEnd countConfigPairedEnd countConfigPairedEnd,ANY-method countConfigSingleEnd countConfigSingleEnd,ANY-method getBamsignalsFilter getFilter getFilter,NormRCountConfig-method getNormRCountConfigFilter NormRCountConfig NormRCountConfig-class print,NormRCountConfig-method show,NormRCountConfig-method
Container for a fit done with normR	exportR exportR,NormRFit,character-method getClasses getClasses,NormRFit-method getCounts getCounts,NormRFit-method getEnrichment getEnrichment,NormRFit-method getPosteriors getPosteriors,NormRFit-method getPvalues getPvalues,NormRFit-method getQvalues getQvalues,NormRFit-method getRanges getRanges,NormRFit-method length,NormRFit-method NormRFit NormRfit normRFit normrfit NormRFit-class plot,NormRFit,missing-method plot.NormRFit print,NormRFit-method show,NormRFit-method summary,NormRFit-method
Regime Enrichment Calling for ChIP-seq data in normR with regimeR	regimeCall RegimeCalling regimeR regimer regimeR,character,character,character,numeric-method regimeR,character,character,data.frame,numeric-method regimeR,character,character,GenomicRanges,numeric-method regimeR,integer,integer,GenomicRanges,numeric-method regimeR-generic