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PERFect

This is the development version of PERFect; for the stable release version, see PERFect.

Permutation filtration for microbiome data


Bioconductor version: Development (3.19)

PERFect is a novel permutation filtering approach designed to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds, and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering.

Author: Ekaterina Smirnova <ekaterina.smirnova at vcuhealth.org>, Quy Cao <quy.cao at umontana.edu>

Maintainer: Quy Cao <quy.cao at umontana.edu>

Citation (from within R, enter citation("PERFect")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("PERFect")

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("PERFect")
Method Illustration HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Metagenomics, Microbiome, Sequencing, Software
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License Artistic-2.0
Depends R (>= 3.6.0), sn (>= 1.5.2)
Imports ggplot2 (>= 3.0.0), phyloseq(>= 1.28.0), zoo (>= 1.8.3), psych (>= 1.8.4), stats (>= 3.6.0), Matrix (>= 1.2.14), fitdistrplus (>= 1.0.12), parallel (>= 3.6.0)
System Requirements
URL https://github.com/cxquy91/PERFect
Bug Reports https://github.com/cxquy91/PERFect/issues
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Suggests knitr, rmarkdown, kableExtra, ggpubr
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package PERFect_1.17.0.tar.gz
Windows Binary PERFect_1.17.1.zip
macOS Binary (x86_64) PERFect_1.17.1.tgz
macOS Binary (arm64) PERFect_1.17.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/PERFect
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PERFect
Bioc Package Browser https://code.bioconductor.org/browse/PERFect/
Package Short Url https://bioconductor.org/packages/PERFect/
Package Downloads Report Download Stats