ccrepe
ccrepe_and_nc.score
Bioconductor version: Release (3.19)
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 <emh146 at mail.harvard.edu>,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("ccrepe")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ccrepe")
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("ccrepe")| ccrepe | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bioinformatics, ImmunoOncology, Metagenomics, Software, Statistics |
| Version | 1.40.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10.5 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | infotheo (>= 1.1) |
| System Requirements | |
| URL |
See More
| Suggests | knitr, BiocStyle, BiocGenerics, testthat, RUnit |
| Linking To | |
| Enhances | |
| 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 | ccrepe_1.40.0.tar.gz |
| Windows Binary (x86_64) | ccrepe_1.40.0.zip (64-bit only) |
| macOS Binary (x86_64) | ccrepe_1.40.0.tgz |
| macOS Binary (arm64) | ccrepe_1.40.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ccrepe |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ccrepe |
| Bioc Package Browser | https://code.bioconductor.org/browse/ccrepe/ |
| Package Short Url | https://bioconductor.org/packages/ccrepe/ |
| Package Downloads Report | Download Stats |