TL;DR (Too long; didn't read) | Introduction to normR | Toy Examples | enrichR(): Calling Enrichment with an Input Control | Analyzing Results | Exporting Results | diffR(): Calling Differential Enrichment without a Control Experiment | regimeR(): Identify Enrichment Regimes in ChIP-seq Experiments | Advanced Topics | Change Read Counting Strategy with NormRCountConfig-class | Analyzing Predefined Regions | Post-processing of Difference Calls with CNV information
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
normr/json (API)
| # 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
On BioConductor:normr-1.39.2(bioc 3.24)normr-1.38.1(bioc 3.23)
bayesiandifferentialpeakcallingclassificationdataimportchipseqripseqfunctionalgenomicsgeneticsmultiplecomparisonnormalizationpeakdetectionpreprocessingalignmentcppopenmp
Last updated from:f2ac4d8bc9. Checks:12 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 239 | ||
| linux-devel-arm64 | WARNING | 324 | ||
| linux-devel-x86_64 | WARNING | 380 | ||
| source / vignettes | OK | 315 | ||
| linux-release-arm64 | WARNING | 346 | ||
| linux-release-x86_64 | WARNING | 350 | ||
| macos-release-arm64 | WARNING | 190 | ||
| macos-release-x86_64 | WARNING | 434 | ||
| macos-oldrel-arm64 | WARNING | 291 | ||
| macos-oldrel-x86_64 | WARNING | 429 | ||
| windows-devel | WARNING | 345 | ||
| windows-release | WARNING | 329 | ||
| windows-oldrel | WARNING | 313 | ||
| wasm-release | OK | 195 |
Exports:countConfigPairedEndcountConfigSingleEnddiffRenrichRexportRgetClassesgetCountsgetEnrichmentgetFiltergetPosteriorsgetPvaluesgetQvaluesgetRangesplotprintregimeRshowsummary
Dependencies:abindaskpassbamsignalsBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayoncurlDelayedArrayfarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslplyrqvalueR6RColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsysUCSC.utilsvctrsviridisLitewithrXMLXVectoryaml
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 |
