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PERFect

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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

Reference Manual PDF

Details

biocViews Classification, Metagenomics, Microbiome, Sequencing, Software
Version 1.17.1
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
Windows Binary PERFect_1.17.1.zip
macOS Binary (x86_64) PERFect_1.17.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/PERFect
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PERFect
Package Short Url https://bioconductor.org/packages/PERFect/
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