PIUMA
Phenotypes Identification Using Mapper from topological data Analysis
Bioconductor version: 3.24 · Package version: 1.9.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
The PIUMA package offers a tidy pipeline of Topological Data Analysis frameworks to identify and characterize communities in high and heterogeneous dimensional data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PIUMA")Details
| Maintainer | Mattia Chiesa <mattia.chiesa@cardiologicomonzino.it> |
| Author | Mattia Chiesa [aut, cre] (ORCID: <https://orcid.org/0000-0001-7427-9954>), Arianna Dagliati [aut] (ORCID: <https://orcid.org/0000-0002-5041-0409>), Alessia Gerbasi [aut] (ORCID: <https://orcid.org/0000-0003-4501-1777>), Giuseppe Albi [aut], Laura Ballarini [aut], Luca Piacentini [aut] (ORCID: <https://orcid.org/0000-0003-1022-4481>), Carlo Leonardi [aut] (ORCID: <https://orcid.org/0000-0001-5348-8300>) |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/BioinfoMonzino/PIUMA |
| Bug Reports | https://github.com/BioinfoMonzino/PIUMA/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, Clustering, DimensionReduction, GraphAndNetwork, Network, Software |
| Package Short Url | https://bioconductor.org/packages/PIUMA/ |
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 1.9.0, https://bioconductor.org/packages/PIUMA.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- The PIUMA package - Phenotypes Identification Using Mapper from topological data Analysis
- Topology-based Clustering in Seurat
Download
Follow the installation instructions to use this package in your R session.
| Source package | PIUMA_1.9.0.tar.gz |
| Windows binary (x86_64) | PIUMA_1.9.0.zip |
| macOS binary (arm64) | PIUMA_1.9.0.tgz |
| macOS binary (x86_64) | PIUMA_1.9.0.tgz |
Dependencies
Depends: R (>= 4.3)
Imports: Hmisc, igraph, patchwork, scales, utils, cluster, umap, tsne, kernlab, vegan, dbscan, grDevices, stats, methods, SummarizedExperiment, ggplot2
Suggests: BiocStyle, testthat, knitr, rmarkdown, Seurat, SingleCellExperiment, aricode, mclust, viridis, magick, ggrepel, dplyr