DOI: 10.18129/B9.bioc.PERFect  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see PERFect.

Permutation filtration for microbiome data

Bioconductor version: 3.16

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>, Quy Cao <quy.cao at>

Maintainer: Quy Cao <quy.cao at>

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


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Method Illustration
PDF   Reference Manual
Text   NEWS


biocViews Classification, Metagenomics, Microbiome, Sequencing, Software
Version 1.12.0
In Bioconductor since BioC 3.10 (R-3.6) (3.5 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)
Suggests knitr, rmarkdown, kableExtra, ggpubr
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_1.12.0.tar.gz
Windows Binary
macOS Binary (x86_64) PERFect_1.12.0.tgz
macOS Binary (arm64) PERFect_1.12.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: