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HIPPO

Heterogeneity-Induced Pre-Processing tOol

Bioconductor version: 3.24 · Package version: 1.25.0

For scRNA-seq data, it selects features and clusters the cells simultaneously for single-cell UMI data. It has a novel feature selection method using the zero inflation instead of gene variance, and computationally faster than other existing methods since it only relies on PCA+Kmeans rather than graph-clustering or consensus clustering.

Installation

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

BiocManager::install("HIPPO")

Details

MaintainerTae Kim <tk382@uchicago.edu>
AuthorTae Kim [aut, cre], Mengjie Chen [aut]
LicenseGPL (>=2)
URLhttps://github.com/tk382/HIPPO
Bug Reportshttps://github.com/tk382/HIPPO/issues
Downloads rank352
Source branchdevel
biocViewsClustering, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageHIPPO_1.25.0.tar.gz
Windows binary (x86_64)HIPPO_1.25.0.zip
macOS binary (arm64)HIPPO_1.25.0.tgz
macOS binary (x86_64)HIPPO_1.25.0.tgz
Dependencies

Depends: R (>= 3.6.0)

Imports: ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap, dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment, ggrepel

Suggests: knitr, rmarkdown