PIUMA

Phenotypes Identification Using Mapper from topological data Analysis


Bioconductor version: Release (3.19)

The PIUMA package offers a tidy pipeline of Topological Data Analysis frameworks to identify and characterize communities in high and heterogeneous dimensional data.

Author: Mattia Chiesa [aut, cre] , Arianna Dagliati [aut] , Alessia Gerbasi [aut] , Giuseppe Albi [aut], Laura Ballarini [aut], Luca Piacentini [aut]

Maintainer: Mattia Chiesa <mattia.chiesa at cardiologicomonzino.it>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("PIUMA")

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("PIUMA")
PIUMA package HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Classification, Clustering, DimensionReduction, GraphAndNetwork, Network, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-3 + file LICENSE
Depends R (>= 4.3), ggplot2
Imports cluster, umap, tsne, kernlab, vegan, dbscan, igraph, scales, Hmisc, patchwork, grDevices, stats, methods, SummarizedExperiment
System Requirements
URL https://github.com/BioinfoMonzino/PIUMA
Bug Reports https://github.com/BioinfoMonzino/PIUMA/issues
See More
Suggests BiocStyle, knitr, testthat, rmarkdown
Linking To
Enhances
Depends On Me
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Build Report Build Report

Package Archives

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

Source Package PIUMA_1.0.0.tar.gz
Windows Binary PIUMA_1.0.0.zip
macOS Binary (x86_64) PIUMA_1.0.0.tgz
macOS Binary (arm64) PIUMA_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PIUMA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PIUMA
Bioc Package Browser https://code.bioconductor.org/browse/PIUMA/
Package Short Url https://bioconductor.org/packages/PIUMA/
Package Downloads Report Download Stats