Package: normr 1.33.0

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]

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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-1.33.0(bioc 3.21)normr-1.32.0(bioc 3.20)

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

5.93 score 11 stars 13 scripts 288 downloads 18 exports 82 dependencies

Last updated 2 months agofrom:828cac9f07. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 13 2024
R-4.5-win-x86_64	WARNING	Dec 13 2024
R-4.5-linux-x86_64	WARNING	Dec 13 2024
R-4.4-win-x86_64	WARNING	Dec 13 2024
R-4.4-mac-x86_64	WARNING	Dec 13 2024
R-4.4-mac-aarch64	WARNING	Dec 13 2024
R-4.3-win-x86_64	WARNING	Dec 13 2024
R-4.3-mac-x86_64	WARNING	Dec 13 2024
R-4.3-mac-aarch64	WARNING	Dec 13 2024

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 BiocGenerics BiocIO BiocParallel Biostrings bitops cli codetools colorspace cpp11 crayon curl DelayedArray fansi farver formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig plyr qvalue R6 RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml zlibbioc

Introduction to the normR package

Johannes Helmuth

Rendered fromnormr.Rmdusingknitr::rmarkdownon Dec 13 2024.

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