Package: FEAST 1.15.0

Kenong Su

FEAST: FEAture SelcTion (FEAST) for Single-cell clustering

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.

Authors:Kenong Su [aut, cre], Hao Wu [aut]

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FEAST.pdf |FEAST.html
FEAST/json (API)
NEWS

# Install 'FEAST' in R:
install.packages('FEAST', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/suke18/feast/issues

Datasets:
  • Y - An example single cell count expression matrix
  • trueclass - An example single cell dataset for the cell label information

On BioConductor:FEAST-1.15.0(bioc 3.21)FEAST-1.14.0(bioc 3.20)

sequencingsinglecellclusteringfeatureextraction

5.86 score 10 stars 36 scripts 230 downloads 87 mentions 15 exports 116 dependencies

Last updated 23 days agofrom:169e89210a. Checks:OK: 1 WARNING: 6 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-win-x86_64WARNINGNov 06 2024
R-4.5-linux-x86_64WARNINGNov 06 2024
R-4.4-win-x86_64WARNINGNov 06 2024
R-4.4-mac-x86_64WARNINGNov 06 2024
R-4.4-mac-aarch64NOTENov 06 2024
R-4.3-win-x86_64WARNINGNov 06 2024
R-4.3-mac-x86_64WARNINGNov 06 2024
R-4.3-mac-aarch64NOTENov 06 2024

Exports:align_CellTypecal_F2cal_MSEConsensuseval_ClusterFEASTFEAST_fastNorm_Yprocess_YSC3_ClustSelect_Model_short_SC3Select_Model_short_TSCANsetUp_BPPARAMTSCAN_ClustVisual_Rslt

Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocParallelbitopsbslibcachemcaToolsclasscliclustercodetoolscolorspacecombinatcommonmarkcpp11crayoncurlDelayedArrayDEoptimRdigestdoParalleldoRNGe1071fansifarverfastICAfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshtmltoolshttpuvhttrigraphIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothlabelinglambda.rlaterlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimemunsellmvtnormnlmeopensslpcaPPpheatmappillarpkgconfigplyrpromisesproxyR6rappdirsRColorBrewerRcppRcppArmadillorlangrngtoolsrobustbaseROCRrrcovS4ArraysS4VectorssassSC3scalesshinySingleCellExperimentsnowsourcetoolsSparseArraySummarizedExperimentsystibbleTrajectoryUtilsTSCANUCSC.utilsutf8vctrsviridisLitewithrWriteXLSxtableXVectorzlibbioc

The FEAST User's Guide

Rendered fromFEAST.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2021-09-09
Started: 2021-03-15