FEAST
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see FEAST.
FEAture SelcTion (FEAST) for Single-cell clustering
Bioconductor version: 3.13
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 "4.1") 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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, FeatureExtraction, Sequencing, SingleCell, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 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_1.0.0.tar.gz |
| Windows Binary | FEAST_1.0.0.zip |
| macOS 10.13 (High Sierra) | FEAST_1.0.0.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 |
| Old Source Packages for BioC 3.13 | Source Archive |