Package index • STID

All functions

AddInfo(): Add information to STID object
AddMetaColumn(): Add columns to existing metadata
AddMetaData(): Add metadata to STID object
AddMSNicheCells(): Add columns to MultiSampNiche cells
AddSSNicheCells(): Add columns to SingleSampNiche cells
AddSSNicheGenes(): Add annotations to SingleSampNiche genes
anno_SingleR(): Annotate Cell Types Using SingleR
as.Seurat(<STID>): Convert STID object to Seurat object
as.STID(): Convert Seurat object to STID object
CalSampCAI(): Calculate Niche Aggregation Index
CalSampCellComm(): Calculate Niche Cell Communication using CellChat
CalSampCoLoc(): Calculate Niche Co-localization
CalSampComp(): Calculate Niche Cell Type Composition
CalSampDEGs(): Calculate Niche Differential Expression Genes
CalSampGeneCor(): Calculate Niche Gene Expression Correlations
CalSampGeneTrend(): Calculate gene expression trends across time points
CalSampGRN(): Calculate Niche Gene Regulatory Networks using NicheNet
CalSampOSE(): Calculate Spatial Organization Entropy (OSE) for samples
CalSampPathoTrack(): Calculate pathogen tracking across samples
CalSampPPI(): Predict Niche Protein-Protein Interactions
clog() clog_start() clog_end() clog_check() clog_SS() clog_MS() clog_step() clog_loop() clog_normal() clog_title() clog_warn() clog_error(): Logging functions for pipeline execution
COLOR_DIS_CON COLOR_LIST: Predefined color palettes
CompareNiche(): Compare two niche detection results
configure_conda(): Configure Python Conda Environment
CorrectBackground(): Correct background expression in spatial transcriptomics data
CreateMultiSampNiche() CreateMSNiche(): Create a MultiSampNiche object for cross-sample comparison
CreateSingleSampNiche() CreateSSNiche(): Create a SingleSampNiche object from analysis results
CreateSTIDObject(): Convert Seurat object to STID object
GeneEnrichment(): Perform Gene Enrichment Analysis (GO/KEGG or GSEA)
Gene_Geneset: Gene and Geneset File Structure
GetCoordInfo(): Get coordinate-related column names
GetGeneStat(): Calculate summary statistics for selected genes
GetInfo(): Get information from STID object
GetMetaData(): Get metadata from STID object
GetMetaInfo(): Get metadata information
GetMSNicheCells(): Get MultiSampNiche cells
GetMSNicheGenes(): Get MultiSampNiche genes
GetMSNicheInfo(): Get MultiSampNiche information
GetSapThreshold(): Retrieve sample-specific thresholds from previous analyses
GetSSNicheCells(): Get SingleSampNiche cells
GetSSNicheGenes(): Get SingleSampNiche genes
GetSSNicheInfo(): Get SingleSampNiche information
GetTopGenes(): Identify top expressed genes in the dataset
get_STID_globals(): Get STID global constants
get_STID_options(): Get STID options
GOID2Genelist(): Convert GO IDs to Gene Lists
h5ad2rds(): Convert AnnData h5ad file to Seurat rds file
MultiSampNiche-class MultiSampNiche: The MultiSampNiche Class
NicheDetect_Lasso(): Interactive lasso selection for ROI (Region of Interest) detection
NicheDetect_Spot(): Spot-level niche detection
NicheDetect_STS(): Automated ROI detection using density-based spatial clustering
NicheExpand(): Expand niche regions based on distance threshold
parse_gtf(): Parse GTF File into Tidy Data Frame
Plot_DistLine_Exp(): Plot Gene Expression Along Distance from Niche Center
Plot_DistLine_Ratio(): Plot Cell Type Ratio Along Distance from Niche Center
Plot_NicheCellComm(): Plot Niche Cell Communication Results
Plot_Spatial(): Create spatial plots for STID data
Plot_SpatialCoLoc(): Plot Spatial Co-localization
print(<STID>): Print method for STID objects
rds2h5ad(): Convert Seurat rds file to AnnData h5ad file
RemoveMetaColumn(): Remove columns from existing metadata
RemoveMetaData(): Remove metadata from STID object
SetInfo(): Set information in STID object
Seurat_pipeline(): Standard Seurat Analysis Pipeline for Spatial Transcriptomics
SingleSampNiche-class SingleSampNiche: The SingleSampNiche Class
SpotDetect_Gene(): Detect infection spots based on individual gene expression
SpotDetect_Geneset(): Detect infection spots based on gene set scores
STID-class STID: The STID Class
STID_analysis-class STID_analysis: The STID_analysis Class
theme_common(): Common analysis theme
theme_spatial(): Spatial plot theme