ccrepe: ccrepe_and_nc.score

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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@mail.harvard.edu>,Craig Bielski<craig.bielski@gmail.com>, George Weingart<george.weingart@gmail.com>
Date of publication
None
Maintainer
Emma Schwager <emma.schwager@gmail.com>,Craig Bielski<craig.bielski@gmail.com>, George Weingart<george.weingart@gmail.com>
License
MIT + file LICENSE
Version
1.10.0

View on Bioconductor

Man pages

ccrepe
Calculates compositionality-corrected p-values and q-values...
ccrepe-package
A package for analysis of sparse compositional data. Allows...
ccrepeSampleTestFunction
ccrepeSampleTestFunction - Simple example of a test measurent...
nc.score
nc.score

Files in this package

ccrepe/DESCRIPTION
ccrepe/LICENSE
ccrepe/NAMESPACE
ccrepe/R
ccrepe/R/ccrepe.R
ccrepe/R/ccrepe.utilities.R
ccrepe/R/ccrepeSampleTestFunction.R
ccrepe/R/nc.score.R
ccrepe/R/nc.score.utilities.R
ccrepe/build
ccrepe/build/vignette.rds
ccrepe/inst
ccrepe/inst/NEWS
ccrepe/inst/doc
ccrepe/inst/doc/ccrepe.R
ccrepe/inst/doc/ccrepe.Rnw
ccrepe/inst/doc/ccrepe.pdf
ccrepe/inst/unitTests
ccrepe/inst/unitTests/test_ccrepe.R
ccrepe/inst/unitTests/test_nc_score.R
ccrepe/man
ccrepe/man/ccrepe-package.Rd
ccrepe/man/ccrepe.Rd
ccrepe/man/ccrepeSampleTestFunction.Rd
ccrepe/man/nc.score.Rd
ccrepe/tests
ccrepe/tests/nc_score_input_test.txt
ccrepe/tests/runTests.R
ccrepe/vignettes
ccrepe/vignettes/ccrepe.Rnw
ccrepe/vignettes/ccrepe.bib