Man pages for zh542370159/SCP
Single Cell Pipeline
| adata_to_srt | Convert an anndata object to a seurat object using reticulate |
| adjcolors | Convert a color with arbitrary transparency to a fixed color |
| AnnotateFeatures | AnnotateFeatures Annotate features in a Seurat object with... |
| as_matrix | Attempts to turn a dgCMatrix into a dense matrix |
| BBKNN_integrate | BBKNN_integrate |
| blendcolors | Blend colors |
| capitalize | Capitalizes the characters Making the first letter uppercase |
| CC_GenePrefetch | Prefetch cycle gene |
| CellCorHeatmap | CellCorHeatmap |
| CellDensityPlot | CellDensityPlot |
| CellDimPlot | Visualize cell groups on a 2-dimensional reduction plot |
| CellDimPlot3D | 3D-Dimensional reduction plot for cell classification... |
| CellScoring | CellScoring |
| CellStatPlot | Statistical plot of cells |
| check_DataType | Check and report the type of data |
| check_Python | Check and install python packages |
| check_R | Check and install R packages |
| check_srtList | Check and preprocess a list of seurat objects |
| check_srtMerge | Check and preprocess a merged seurat object |
| ComBat_integrate | Combat_integrate |
| compute_velocity_on_grid | Compute velocity on grid The original python code is on... |
| conda_install | Installs a list of packages into a specified conda... |
| conda_python | Find the path to Python associated with a conda environment |
| Conos_integrate | Conos_integrate |
| CreateDataFile | CreateDataFile |
| CreateMetaFile | CreateMetaFile |
| CSS_integrate | CSS_integrate |
| db_DoubletDetection | Run doublet-calling with DoubletDetection |
| db_scDblFinder | Run doublet-calling with scDblFinder |
| db_scds | Run doublet-calling with scds |
| db_Scrublet | Run doublet-calling with Scrublet |
| DefaultReduction | Find the default reduction name in a Seurat object. |
| download | Download File from the Internet |
| drop_data | Drop all data in the plot (only one observation is kept) |
| DynamicHeatmap | Heatmap plot for dynamic features along lineages |
| DynamicPlot | DynamicPlot |
| EnrichmentPlot | EnrichmentPlot |
| env_exist | Check if a conda environment exists |
| Env_requirements | Env_requirements function |
| exist_Python_pkgs | Check if the python package exists in the environment |
| fastMNN_integrate | fastMNN_integrate |
| FeatureCorPlot | Features correlation plot This function creates a correlation... |
| FeatureDimPlot | Visualize feature values on a 2-dimensional reduction plot |
| FeatureDimPlot3D | 3D-Dimensional reduction plot for gene expression... |
| FeatureHeatmap | FeatureHeatmap |
| FeatureStatPlot | Statistical plot of features |
| FetchH5 | Fetch data from the hdf5 file |
| find_conda | Find an appropriate conda binary |
| GeneConvert | Gene ID conversion function using biomart |
| geom_alluvial | geom_alluvial |
| geom_alluvial_label | geom_alluvial_label |
| geom_sankey | geom_sankey |
| geom_sankey_bump | geom_sankey_bump |
| geom_sankey_label | geom_sankey_label |
| get_vars | Get used vars in a ggplot object |
| GraphPlot | GraphPlot |
| GroupHeatmap | GroupHeatmap |
| GSEAPlot | GSEA Plot |
| Harmony_integrate | Harmony_integrate |
| ifnb_sub | A subsetted version of 'ifnb' datasets |
| installed_Python_pkgs | Show all the python packages in the environment |
| Integration_SCP | Integration_SCP |
| invoke | Invoke a function with a list of arguments |
| isOutlier | Detect outliers using MAD(Median Absolute Deviation) method |
| iterchunks | Generate a iterator along chunks of a vector |
| lifemap_cell | Embryonic Development Database from LifeMap Discovery |
| LIGER_integrate | LIGER_integrate |
| LineagePlot | LineagePlot |
| ListDB | ListDB |
| make_long | make_long |
| MNN_integrate | MNN_integrate |
| PAGAPlot | PAGA plot |
| palette_list | A list of palettes for use in data visualization |
| palette_scp | Color palettes collected in SCP. |
| panc8_sub | A subsetted version of human 'panc8' datasets |
| pancreas_sub | A subsetted version of mouse 'pancreas' datasets |
| panel_fix | Set the panel width/height of a plot object to a fixed value. |
| PrepareDB | Prepare the gene annotation databases |
| PrepareEnv | This function prepares the SCP Python environment by... |
| PrepareSCExplorer | Prepare Seurat objects for the SCExplorer |
| ProjectionPlot | Projection Plot |
| RecoverCounts | Attempt to recover raw counts from the normalized matrix. |
| reexports | Objects exported from other packages |
| ref_scHCL | Reference datasets for cell type annotation in single-cell... |
| RenameClusters | Rename clusters for the Seurat object |
| RenameFeatures | Rename features for the Seurat object |
| RunCellQC | Run cell-level quality control for single cell RNA-seq data. |
| RunCSSMap | Single-cell reference mapping with CSS method |
| RunDEtest | Differential gene test |
| RunDimReduction | Run dimensionality reduction |
| RunDM | Run DM (diffusion map) |
| RunDoubletCalling | Run doublet-calling for single cell RNA-seq data. |
| RunDynamicEnrichment | RunDynamicEnrichment |
| RunDynamicFeatures | RunDynamicFeatures |
| RunEnrichment | Perform the enrichment analysis (over-representation) on the... |
| RunFR | Run Force-Directed Layout (Fruchterman-Reingold algorithm) |
| RunGLMPCA | Run GLMPCA (generalized version of principal components... |
| RunGSEA | Perform the enrichment analysis (GSEA) on the genes |
| RunHarmony2 | Run Harmony algorithm |
| RunKNNMap | Single-cell reference mapping with KNN method |
| RunKNNPredict | RunKNNPredict |
| RunLargeVis | Run LargeVis (Dimensionality Reduction with a LargeVis-like... |
| RunMDS | Run MDS (multi-dimensional scaling) |
| RunMonocle2 | Run Monocle2 analysis |
| RunMonocle3 | Run Monocle3 analysis |
| RunNMF | Run NMF (non-negative matrix factorization) |
| RunPaCMAP | Run PaCMAP (Pairwise Controlled Manifold Approximation) |
| RunPAGA | Run PAGA analysis |
| RunPalantir | Run Palantir analysis |
| RunPCAMap | Single-cell reference mapping with PCA method |
| RunPHATE | Run PHATE (Potential of Heat-diffusion for Affinity-based... |
| RunSCExplorer | RunSCExplorer |
| RunScmap | Annotate single cells using scmap. |
| RunSCVELO | Run scVelo workflow |
| RunSeuratMap | Single-cell reference mapping with Seurat method |
| RunSingleR | Annotate single cells using SingleR |
| RunSlingshot | RunSlingshot |
| RunSymphonyMap | Single-cell reference mapping with Symphony method |
| RunTriMap | Run TriMap (Large-scale Dimensionality Reduction Using... |
| RunUMAP2 | Run UMAP (Uniform Manifold Approximation and Projection) |
| RunWOT | Run WOT analysis |
| Scanorama_integrate | Scanorama_integrate |
| scVI_integrate | scVI_integrate |
| segementsDf | Shorten and offset the segment |
| Seurat_integrate | Seurat_integrate |
| show_palettes | Show the color palettes |
| slim_data | Drop unused data from the plot to reduce the object size |
| SrtAppend | Append a Seurat object to another |
| SrtReorder | Reorder idents by the gene expression |
| srt_to_adata | Convert a seurat object to an anndata object using reticulate |
| Standard_SCP | Standard SCP |
| StatPlot | StatPlot |
| theme_blank | Blank theme |
| theme_sankey | sankey_themes |
| theme_scp | SCP theme |
| tochunks | Split a vector into the chunks |
| try_get | Try to evaluate an expression a set number of times before... |
| Uncorrected_integrate | Uncorrected_integrate |
| unnest | Implement similar functions to the 'unnest' function in the... |
| VelocityPlot | Velocity Plot |
| VolcanoPlot | VolcanoPlot |
| words_excluded | Excluded words in keyword enrichment analysis and extraction |
