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

Permutation filtration for microbiome data

Bioconductor version: Release (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>, 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 "4.4") and enter:

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


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


Reference Manual PDF


biocViews Classification, Metagenomics, Microbiome, Sequencing, Software
Version 1.18.0
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)
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