This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

FEAST

FEAture SelcTion (FEAST) for Single-cell clustering

Bioconductor version: Release (3.17)

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 (from within R, enter citation("FEAST")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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 PDF
NEWS Text

Details

biocViews Clustering, FeatureExtraction, Sequencing, SingleCell, Software
Version 1.8.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL-2
Depends R (>= 4.1), mclust, BiocParallel, SummarizedExperiment
Imports SingleCellExperiment, methods, stats, utils, irlba, TSCAN, SC3, matrixStats
Linking To
Suggests rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle
System Requirements
Enhances
URL
Bug Reports https://github.com/suke18/FEAST/issues
See More
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 FEAST_1.8.0.tar.gz
Windows Binary FEAST_1.8.0.zip (64-bit only)
macOS Binary (x86_64) FEAST_1.8.0.tgz
macOS Binary (arm64) FEAST_1.8.0.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