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Showing content from http://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/normr.html below:

Bioconductor - normr (development version)

normr

This is the development version of normr; for the stable release version, see normr.

Normalization and difference calling in ChIP-seq data

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews Alignment, Bayesian, ChIPSeq, Classification, DataImport, DifferentialPeakCalling, FunctionalGenomics, Genetics, MultipleComparison, Normalization, PeakDetection, Preprocessing, RIPSeq, Software Version 1.35.0 In Bioconductor since BioC 3.4 (R-3.3) (8.5 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 See More Package Archives

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

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