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HIPPO

Heterogeneity-Induced Pre-Processing tOol


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews Clustering, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
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Suggests knitr, rmarkdown
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Package Archives

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

Source Package HIPPO_1.14.0.tar.gz
Windows Binary HIPPO_1.14.0.zip
macOS Binary (x86_64) HIPPO_1.14.0.tgz
macOS Binary (arm64) HIPPO_1.14.0.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/
Package Downloads Report Download Stats