NEWS.md

sclet 0.0.4

• re-export scuttle::logNormCounts() and scuttle::perCellQCMetrics(() (2024-10-08, Tue)
• Import 'Matrix' for calculate stats of SparseMatrix (2024-10-07, Mon)
• re-export aplot::plot_list() (2024-10-06, Sun)

sclet 0.0.3

• Adding cell-cell communication module. (2024-10-06, Sun)
  • runCellChat() wrapper function for running CellChat.
• gene_summary_table() to add gene summary information to marker gene table (2024-10-02, Wed)

sclet 0.0.2

• FindMarkers() and FindAllMarkers() (2024-10-02, Wed)
• remove vignettes and host online book (2024-10-01, Tue)
  • https://yulab-smu.top/sclet
• re-export scater::plotColData()
• QCMetrics() function to add seurat-like QC metrics ('nFeature_RNA' and 'nCount_RNA' to 'SingleCellExperiment' object)

sclet 0.0.1

• Seurat-like functions for SingleCellExperiment (2024-09-20, Fri)
  • Read10X()
  • PercentageFeatureSet()
  • VlnPlot()
  • FeatureScatter()
  • subset()
  • NormalizeData()
  • FindVariableFeatures()
  • VariableFeatures()
  • VariableFeaturePlot()
  • ScaleData()
  • ElbowPlot()
  • FindNeighbors()
  • FindClusters()
  • Idents()
  • RenameIdents()
  • RunUMAP()
• re-export:
  • SummarizedExperiment::colData()
  • SummarizedExperiment::rowData()
  • SummarizedExperiment::assay()
  • scater::runPCA()