Package index • scop

check_python(): Check and install python packages
check_r(): Check and install R packages
conda_install(): Enhanced conda installation
conda_python(): Find the path to Python associated with a conda environment
env_exist(): Check if a conda environment exists
env_info(): Print environment information
env_requirements(): Python environment requirements
exist_python_pkgs(): Check if the python package exists in the environment
find_conda(): Find an appropriate conda binary
install_miniconda2(): Enhanced miniconda installation
installed_python_pkgs(): Show all the python packages in the environment
ListEnv(): List conda environments
PrepareEnv(): Prepare the virtual environment
remove_python(): Remove Python packages from conda environment
remove_r(): Check and remove R packages
RemoveEnv(): Remove a conda environment

adata_to_srt(): Convert an anndata object to a seurat object using reticulate
CellScoring(): Cell scoring
CheckDataType(): Check and report the type of data in Seurat object
CheckDataList(): Check and preprocess a list of Seurat objects
CheckDataMerge(): Check and preprocess a merged seurat object
CycGenePrefetch(): Prefetch cell cycle genes
DefaultReduction(): Find the default reduction name in a Seurat object
FetchDataZero(): FetchData but with zeroes for unavailable genes
GeneConvert(): Gene ID conversion function using biomart
GetAssayData5(): Get expression data from Assay5 or Seurat object
is_outlier(): Detect outliers using MAD (Median Absolute Deviation)
RecoverCounts(): Attempt to recover raw counts from the normalized matrix
RenameClusters(): Rename clusters for the Seurat object
srt_append(): Append a Seurat object to another
srt_to_adata(): Convert a Seurat object to an AnnData object
srt_reorder(): Reorder idents by the gene expression

AddFeaturesData(): Add features data
AnnotateFeatures(): Annotate Features
GetFeaturesData(): Get features data
GetSimilarFeatures(): Find genes with expression patterns similar to the genes you've specified.
RenameFeatures(): Rename features for the Seurat object

RunDimReduction(): Run dimensionality reduction
RunDM(): Run DM (diffusion map)
RunFR(): Run Force-Directed Layout (Fruchterman-Reingold algorithm)
RunGLMPCA(): Run GLMPCA (generalized version of principal components analysis)
RunMDS(): Run MDS (multi-dimensional scaling)
RunNMF(): Run NMF (non-negative matrix factorization)
RunUMAP2(): Run UMAP (Uniform Manifold Approximation and Projection)
RunPaCMAP(): Run PaCMAP (Pairwise Controlled Manifold Approximation)
RunTriMap(): Run TriMap (Large-scale Dimensionality Reduction Using Triplets)
RunPHATE(): Run PHATE (Potential of Heat-diffusion for Affinity-based Trajectory Embedding)
RunLargeVis(): Run LargeVis (Dimensionality Reduction with a LargeVis-like method)
RunKNNPredict(): Run KNN prediction

FindExpressedMarkers(): Find Expressed Markers
RunDEtest(): Differential gene test
RunGSEA(): Perform the enrichment analysis (GSEA) on the genes
RunEnrichment(): Perform the enrichment analysis (over-representation) on the genes
RunDynamicEnrichment(): RunDynamicEnrichment
RunProportionTest(): Proportion Test

CellChatPlot(): Plot CellChat analysis results
CellDimPlot(): Cell Dimensional Plot
CellDimPlot3D(): 3D-Dimensional reduction plot for cell classification visualization.
CellDensityPlot(): Cell density plot
CellCorHeatmap(): The Cell Correlation Heatmap
CellStatPlot(): Statistical plot of cells
DynamicPlot(): Plot dynamic features across pseudotime
DynamicHeatmap(): Heatmap plot for dynamic features along lineages
EnrichmentPlot(): Enrichment Plot
FeatureDimPlot(): Visualize feature values on a 2-dimensional reduction plot
FeatureDimPlot3D(): 3D-Dimensional reduction plot for gene expression visualization.
FeatureHeatmap(): Feature Heatmap
FeatureCorPlot(): Features correlation plot
FeatureStatPlot(): Statistical plot of features
GraphPlot(): Graph Plot
GroupHeatmap(): The Group Heatmap
GSEAPlot(): GSEA Plot
LineagePlot(): Lineage Plot
PAGAPlot(): PAGA plot
ProjectionPlot(): Projection Plot
ProportionTestPlot(): Proportion Test Plot
StatPlot(): Statistic Plot
TACSPlot(): Transcript-averaged cell scoring (TACS)
VelocityPlot(): Velocity Plot
VolcanoPlot(): Volcano Plot

ifnb_sub: A subsetted version of 'ifnb' datasets
panc8_sub: A subsetted version of human 'panc8' datasets
pancreas_sub: A subsetted version of mouse 'pancreas' datasets
ref_scHCL ref_scMCA ref_scZCL: Reference datasets for cell type annotation in single-cell RNA data
words_excluded: Excluded words in keyword enrichment analysis and extraction