To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("ccrepe")
In most cases, you don't need to download the package archive at all.
ccrepe
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ccrepe_and_nc.score
Bioconductor version: Release (3.1)
The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets. In microbial abundance data, for example, the total abundances of all microbes sum to one; CCREPE is designed to take this constraint into account when assigning p-values to similarity measures between the microbes. The package has two functions: ccrepe: Calculates similarity measures, p-values and q-values for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data. nc.score: Calculates species-level co-variation and co-exclusion patterns based on an extension of the checkerboard score to ordinal data.
Author: Emma Schwager <emma.schwager at gmail.com>,Craig Bielski<craig.bielski at gmail.com>, George Weingart<george.weingart at gmail.com>
Maintainer: Emma Schwager <emma.schwager at gmail.com>,Craig Bielski<craig.bielski at gmail.com>, George Weingart<george.weingart at gmail.com>
Citation (from within R,
enter citation("ccrepe")):
Installation
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("ccrepe")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ccrepe")
| R Script | ccrepe | |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | Bioinformatics, Metagenomics, Software, Statistics |
| Version | 1.4.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (1.5 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | infotheo (>= 1.1) |
| LinkingTo | |
| Suggests | knitr, BiocStyle, BiocGenerics, testthat |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ccrepe_1.4.0.tar.gz |
| Windows Binary | ccrepe_1.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | ccrepe_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | ccrepe_1.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/ccrepe/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/ccrepe/ |
| Package Downloads Report | Download Stats |
Documentation »
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