HIPPO
This is the development version of HIPPO; for the stable release version, see HIPPO.
Heterogeneity-Induced Pre-Processing tOol
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 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 |
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_1.25.0.tar.gz |
| Windows Binary (x86_64) | HIPPO_1.25.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | HIPPO_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | HIPPO_1.25.0.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 |