Package index • CellProgramMapper

Main Functions

Core functions for mapping cells to gene expression programs

CellProgramMapper(): Map Single Cells to Reference Gene Expression Programs
get_usage(): Extract Usage Matrix from Result
get_scores(): Extract Scores from Result
print(<CellProgramMapperResult>): Print Method for CellProgramMapperResult
summary(<CellProgramMapperResult>): Summary Method for CellProgramMapperResult

Reference Management

Functions for managing reference datasets

available_references(): List Available Pre-built References
load_reference(): Load Reference Spectra
download_reference(): Download Reference to Cache
get_reference_names(): Get Reference Names

Consensus Reference Building

Build consensus GEPs from multiple cNMF results

BuildConsensusReference(): Build Consensus Reference from Multiple cNMF Results
cluster_geps(): Cluster GEPs Based on Correlation Matrix
pairwise_cluster_geps(): Pairwise Cluster GEPs
compute_gep_correlations(): Compute Pairwise GEP Correlations
get_top_genes_per_cgep(): Get Top Genes for Each cGEP
merge_spectra(): Merge Spectra from Multiple Datasets
merge_score_spectra(): Merge Score Spectra
write_consensus_results(): Write Consensus Results to Files

Scoring

Compute add-on scores from usage matrix

compute_scores(): Compute Add-on Scores
compute_external_score(): Compute External Score
create_score_definition(): Create Custom Score Definition
create_score_data(): Create Score Data Structure

Seurat Integration

Functions for Seurat object integration

add_results_to_seurat(): Add Results to Seurat Object
is_seurat(): Check if Object is a Seurat Object
check_seurat_available(): Check Seurat Availability
get_seurat_version(): Get Seurat Package Version
get_counts_from_seurat(): Get Counts Matrix from Seurat Object
get_cells_from_seurat(): Get Cell Names from Seurat Object
get_genes_from_seurat(): Get Gene Names from Seurat Object

Data I/O

Data input/output functions

load_counts(): Load Counts Matrix from Various Formats
load_10x_mtx(): Load 10X MTX Format
load_h5ad(): Load H5AD File
load_h5ad_hdf5r(): Load H5AD using hdf5r
load_text_matrix(): Load Text Matrix (TSV/CSV)
load_tpm_stats(): Load TPM Stats from NPZ File
save_results(): Save Results to Files
decompress_tar(): Decompress tar.gz or tar.bz2 File

NMF Refitting

Core NNLS solver functions

fit_usage(): Fit Usage Matrix Using Non-Negative Least Squares
fit_usage_batched(): Fit Usage in Batches for Large Datasets
prepare_query(): Prepare Query Data for Usage Fitting
scale_columns(): Scale Matrix Columns by Standard Deviation

Utility Functions

Helper functions for data manipulation

row_sums(): Row Sums with Sparse Matrix Support
col_sums(): Column Sums with Sparse Matrix Support
normalize_rows(): Normalize Matrix Rows to Sum to One
is_integer_matrix(): Check if Matrix Contains Integer Values
is_nonnegative_matrix(): Check if Matrix is Non-negative
filter_na_genes(): Filter Reference Genes with NA Values
aggregate_by_cluster(): Aggregate Spectra by Cluster
ensure_dir(): Create Directory if Not Exists
get_cache_dir(): Get Package Cache Directory
msg(): Print Message with Timestamp

Internal

Internal functions (not for direct use)

CellProgramMapper-package: CellProgramMapper: Map Single Cells to Reference Gene Expression Programs
consensus: Build Consensus Reference from Multiple cNMF Results
io: Data Input/Output Functions
mapper: CellProgramMapper - Main Function
nmf_refit: NMF Usage Refitting
reference: Reference Management Functions
scoring: Scoring Functions
seurat_compat: Seurat Compatibility Layer
utils: Utility Functions for CellProgramMapper
zzz: Package Load and Attach Hooks