HIPPO

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see HIPPO.

Heterogeneity-Induced Pre-Processing tOol

Bioconductor version: 3.21

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.

Author: Tae Kim [aut, cre], Mengjie Chen [aut]

Maintainer: Tae Kim <tk382 at uchicago.edu>

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

Installation

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


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

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("HIPPO")

Example analysis HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software

Version 1.20.0

In Bioconductor since BioC 3.11 (R-4.0) (5.5 years)

License GPL (>=2)

Depends R (>= 3.6.0)

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

System Requirements

URL https://github.com/tk382/HIPPO

Bug Reports https://github.com/tk382/HIPPO/issues

Suggests knitr, rmarkdown

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Package Archives

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

Source Package HIPPO_1.20.0.tar.gz

Windows Binary (x86_64) HIPPO_1.20.0.zip (64-bit only)

macOS Binary (x86_64) HIPPO_1.20.0.tgz

macOS Binary (arm64) HIPPO_1.20.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/HIPPO

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HIPPO

Bioc Package Browser https://code.bioconductor.org/browse/HIPPO/

Package Short Url https://bioconductor.org/packages/HIPPO/

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