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:
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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')) |
Bug tracker:https://github.com/suke18/feast/issues
On BioConductor:FEAST-1.15.0(bioc 3.21)FEAST-1.14.0(bioc 3.20)
sequencingsinglecellclusteringfeatureextraction
Last updated 23 days agofrom:169e89210a. Checks:OK: 1 WARNING: 6 NOTE: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 06 2024 |
R-4.5-win-x86_64 | WARNING | Nov 06 2024 |
R-4.5-linux-x86_64 | WARNING | Nov 06 2024 |
R-4.4-win-x86_64 | WARNING | Nov 06 2024 |
R-4.4-mac-x86_64 | WARNING | Nov 06 2024 |
R-4.4-mac-aarch64 | NOTE | Nov 06 2024 |
R-4.3-win-x86_64 | WARNING | Nov 06 2024 |
R-4.3-mac-x86_64 | WARNING | Nov 06 2024 |
R-4.3-mac-aarch64 | NOTE | Nov 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