PERFect
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see PERFect.
Permutation filtration for microbiome data
Bioconductor version: 3.11
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("PERFect")):
Installation
To install this package, start R (version "4.0") 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")| Method Illustration | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Metagenomics, Microbiome, Sequencing, Software |
| Version | 1.2.0 |
| 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) |
| System Requirements | |
| URL | https://github.com/cxquy91/PERFect |
| Bug Reports | https://github.com/cxquy91/PERFect/issues |
See More
| Suggests | knitr, rmarkdown, kableExtra, ggpubr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PERFect_1.2.0.tar.gz |
| Windows Binary | PERFect_1.2.0.zip |
| macOS 10.13 (High Sierra) | PERFect_1.2.0.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 |
| Old Source Packages for BioC 3.11 | Source Archive |