normr
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see normr.
Normalization and difference calling in ChIP-seq data
Bioconductor version: 3.8
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 <helmuth at molgen.mpg.de>
citation("normr")):
Installation
To install this package, start R (version "3.5") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, Bayesian, ChIPSeq, Classification, DataImport, DifferentialPeakCalling, FunctionalGenomics, Genetics, MultipleComparison, Normalization, PeakDetection, Preprocessing, RIPSeq, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 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
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | normr_1.8.0.tar.gz |
| Windows Binary | normr_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | normr_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/normr |
| Source Repository (Developer Access) | git clone [email protected]:packages/normr |
| Bioc Package Browser | https://code.bioconductor.org/browse/normr/ |
| Package Short Url | https://bioconductor.org/packages/normr/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |