PERFect

DOI: 10.18129/B9.bioc.PERFect    

Permutation filtration for microbiome data

Bioconductor version: Release (3.10)

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 "3.6") and enter:

if (!requireNamespace("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")

 

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Details

biocViews Classification, Metagenomics, Microbiome, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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_1.0.0.tar.gz
Windows Binary PERFect_1.0.0.zip
Mac OS X 10.11 (El Capitan) PERFect_1.0.0.tgz
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/
Package Downloads Report Download Stats

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