PIUMA
This is the released version of PIUMA; for the devel version, see PIUMA.
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]
, Arianna Dagliati [aut]
, Alessia Gerbasi [aut]
, Giuseppe Albi [aut], Laura Ballarini [aut], Luca Piacentini [aut]
, Carlo Leonardi [aut]
Maintainer: Mattia Chiesa <mattia.chiesa at cardiologicomonzino.it>
citation("PIUMA")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
See More
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/PIUMA/ |
| Package Short Url | https://bioconductor.org/packages/PIUMA/ |
| Package Downloads Report | Download Stats |