ccrepe
All Bioconductor versions of ccrepe
3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14
ccrepe_and_nc.score
Bioconductor version: 3.23 · Package version: 1.47.0
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
From within R, enter citation("ccrepe"):
Emma Schwager, Craig Bielski, George Weingart. ccrepe: ccrepe_and_nc.score. doi:10.18129/B9.bioc.ccrepe, R package version 1.47.0, https://bioconductor.org/packages/ccrepe.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.47.0 |
| License | MIT + file LICENSE |
| In Bioconductor since | BioC 2.14 (R-3.1) (12 years) |
| Status | Deprecated |
| Downloads rank | 1736 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bioinformatics, ImmunoOncology, Metagenomics, Software, Statistics |
| Package Short Url | https://bioconductor.org/packages/ccrepe/ |
Documentation
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | ccrepe_1.47.0.tar.gz |
| Windows binary (x86_64) | ccrepe_1.47.0.zip |
| Source Repository | git clone https://git.bioconductor.org/packages/ccrepe |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ccrepe |
| Package Downloads Report | Download Stats |