HIPPO
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see HIPPO.
Heterogeneity-Induced Pre-Processing tOol
Bioconductor version: 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>
citation("HIPPO")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software |
| Version | 1.0.0 |
| 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 |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/HIPPO/ |
| Package Short Url | https://bioconductor.org/packages/HIPPO/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |