HIPPO

DOI: 10.18129/B9.bioc.HIPPO    

Heterogeneity-Induced Pre-Processing tOol

Bioconductor version: Release (3.11)

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Example analysis
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.11 (R-4.0) (0.5 years)
License	GPL (>=2)
Depends	R (>= 3.6.0)
Imports	ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap, dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment, ggrepel
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/tk382/HIPPO
BugReports	https://github.com/tk382/HIPPO/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HIPPO_1.0.0.tar.gz
Windows Binary	HIPPO_1.0.0.zip
macOS 10.13 (High Sierra)	HIPPO_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HIPPO
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HIPPO
Package Short Url	https://bioconductor.org/packages/HIPPO/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive