PERFect

DOI: 10.18129/B9.bioc.PERFect  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see PERFect.

Permutation filtration for microbiome data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	Method Illustration
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Metagenomics, Microbiome, Sequencing, Software
Version	1.14.0
In Bioconductor since	BioC 3.10 (R-3.6) (4 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)
LinkingTo
Suggests	knitr, rmarkdown, kableExtra, ggpubr
SystemRequirements
Enhances
URL	https://github.com/cxquy91/PERFect
BugReports	https://github.com/cxquy91/PERFect/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	PERFect_1.14.0.tar.gz
Windows Binary	PERFect_1.14.0.zip
macOS Binary (x86_64)	PERFect_1.14.0.tgz
macOS Binary (arm64)	PERFect_1.14.0.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