To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("normr")
In most cases, you don't need to download the package archive at all.
normr
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see normr.
Normalization and difference calling in ChIP-seq data
Bioconductor version: 3.4
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 (from within R,
enter citation("normr")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("normr")
Documentation
| HTML | R Script | Introduction to the normR package |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, Bayesian, ChIPSeq, Classification, DataImport, DifferentialPeakCalling, FunctionalGenomics, Genetics, MultipleComparison, Normalization, PeakDetection, Preprocessing, RIPSeq, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (0.5 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) |
| LinkingTo | Rcpp |
| Suggests | BiocStyle, testthat (>= 1.0), knitr, rmarkdown |
| SystemRequirements | C++11 |
| Enhances | BiocParallel |
| URL | https://github.com/your-highness/normR |
| BugReports | https://github.com/your-highness/normR/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | normr_1.0.0.tar.gz |
| Windows Binary | normr_1.0.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | normr_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/normr/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/normr/ |
| Package Downloads Report | Download Stats |
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