PIUMA

This is the released version of PIUMA; for the devel version, see PIUMA.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19

Phenotypes Identification Using Mapper from topological data Analysis

Bioconductor version: Release (3.23)

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: 0000-0001-7427-9954 , Arianna Dagliati [aut] ORCID: 0000-0002-5041-0409 , Alessia Gerbasi [aut] ORCID: 0000-0003-4501-1777 , Giuseppe Albi [aut], Laura Ballarini [aut], Luca Piacentini [aut] ORCID: 0000-0003-1022-4481 , Carlo Leonardi [aut] ORCID: 0000-0001-5348-8300

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

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

Mattia Chiesa, Arianna Dagliati, Alessia Gerbasi, Giuseppe Albi, Laura Ballarini, Luca Piacentini, Carlo Leonardi. PIUMA: Phenotypes Identification Using Mapper from topological data Analysis. doi:10.18129/B9.bioc.PIUMA, R package version 1.8.0, https://bioconductor.org/packages/PIUMA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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
PIUMA package and Seurat	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	1.8.0
In Bioconductor since	BioC 3.19 (R-4.4) (2.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.3)
Imports	Hmisc, igraph, patchwork, scales, utils, cluster, umap, tsne, kernlab, vegan, dbscan, grDevices, stats, methods, SummarizedExperiment, ggplot2
System Requirements
URL	https://github.com/BioinfoMonzino/PIUMA
Bug Reports	https://github.com/BioinfoMonzino/PIUMA/issues

Suggests	BiocStyle, testthat, knitr, rmarkdown, Seurat, SingleCellExperiment, aricode, mclust, viridis, magick, ggrepel, dplyr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	PIUMA_1.8.0.tar.gz
Windows Binary (x86_64)	PIUMA_1.8.0.zip
macOS Binary (big-sur-x86_64)	PIUMA_1.8.0.tgz
macOS Binary (sonoma-arm64)	PIUMA_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PIUMA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PIUMA
Package Short Url	https://bioconductor.org/packages/PIUMA/
Package Downloads Report	Download Stats