FEAST
This is the development version of FEAST; for the stable release version, see FEAST.
FEAture SelcTion (FEAST) for Single-cell clustering
Bioconductor version: Development (3.20)
Cell clustering is one of the most important and commonly performed tasks in single-cell RNA sequencing (scRNA-seq) data analysis. An important step in cell clustering is to select a subset of genes (referred to as “features”), whose expression patterns will then be used for downstream clustering. A good set of features should include the ones that distinguish different cell types, and the quality of such set could have significant impact on the clustering accuracy. FEAST is an R library for selecting most representative features before performing the core of scRNA-seq clustering. It can be used as a plug-in for the etablished clustering algorithms such as SC3, TSCAN, SHARP, SIMLR, and Seurat. The core of FEAST algorithm includes three steps: 1. consensus clustering; 2. gene-level significance inference; 3. validation of an optimized feature set.
Author: Kenong Su [aut, cre], Hao Wu [aut]
Maintainer: Kenong Su <kenong.su at emory.edu>
citation("FEAST")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("FEAST")
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("FEAST")
The FEAST User's Guide | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Clustering, FeatureExtraction, Sequencing, SingleCell, Software |
Version | 1.13.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (3.5 years) |
License | GPL-2 |
Depends | R (>= 4.1), mclust, BiocParallel, SummarizedExperiment |
Imports | SingleCellExperiment, methods, stats, utils, irlba, TSCAN, SC3, matrixStats |
System Requirements | |
URL | |
Bug Reports | https://github.com/suke18/FEAST/issues |
See More
Suggests | rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle |
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 | FEAST_1.13.0.tar.gz |
Windows Binary | FEAST_1.13.0.zip |
macOS Binary (x86_64) | FEAST_1.13.0.tgz |
macOS Binary (arm64) | FEAST_1.13.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/FEAST |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/FEAST |
Bioc Package Browser | https://code.bioconductor.org/browse/FEAST/ |
Package Short Url | https://bioconductor.org/packages/FEAST/ |
Package Downloads Report | Download Stats |