normr

This is the released version of normr; for the devel version, see normr.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

Normalization and difference calling in ChIP-seq data

Bioconductor version: Release (3.23)

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]

Maintainer: Johannes Helmuth <johannes.helmuth at laborberlin.com>

Citation (from within R, enter citation("normr")):

Johannes Helmuth, Ho-Ryun Chung. normr: Normalization and difference calling in ChIP-seq data. doi:10.18129/B9.bioc.normr, R package version 1.38.1, https://bioconductor.org/packages/normr.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("normr")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("normr")

Introduction to the normR package	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Bayesian, ChIPSeq, Classification, DataImport, DifferentialPeakCalling, FunctionalGenomics, Genetics, MultipleComparison, Normalization, PeakDetection, Preprocessing, RIPSeq, Software
Version	1.38.1
In Bioconductor since	BioC 3.4 (R-3.3) (10 years)
License	GPL-2
Depends	R (>= 3.3.0)
Imports	methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32)
System Requirements	C++11
URL	https://github.com/your-highness/normR
Bug Reports	https://github.com/your-highness/normR/issues

Suggests	BiocStyle, testthat (>= 1.0), knitr, rmarkdown
Linking To	Rcpp
Enhances	BiocParallel
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	normr_1.38.1.tar.gz
Windows Binary (x86_64)	normr_1.38.1.zip
macOS Binary (big-sur-x86_64)	normr_1.38.1.tgz
macOS Binary (sonoma-arm64)	normr_1.38.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/normr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/normr
Package Short Url	https://bioconductor.org/packages/normr/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive