PIUMA

This is the development version of PIUMA; for the stable release version, see PIUMA.

Phenotypes Identification Using Mapper from topological data Analysis

Bioconductor version: Development (3.21)

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] (ORCID: ), Arianna Dagliati [aut] (ORCID: ), Alessia Gerbasi [aut] (ORCID: ), Giuseppe Albi [aut], Laura Ballarini [aut], Luca Piacentini [aut] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Clustering, DimensionReduction, GraphAndNetwork, Network, Software
Version	1.3.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
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

Suggests	BiocStyle, knitr, testthat, rmarkdown
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	PIUMA_1.3.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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