# Single Cell Counts Matrices to PCA

## Documentation for package ‘BPCells’ version 0.3.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N O P Q R S T W misc

## -- A --

add_cols | Broadcasting vector arithmetic
add_rows | Broadcasting vector arithmetic
all_matrix_inputs | Get/set inputs to a matrix transform
all_matrix_inputs<- | Get/set inputs to a matrix transform
apply_by_col | Apply a function to summarize rows/cols
apply_by_row | Apply a function to summarize rows/cols

## -- B --

binarize | Convert matrix elements to zeros and ones

## -- C --

call_peaks_macs | Call peaks using MACS2/3
call_peaks_tile | Call peaks from tiles
canonical_gene_symbol | Gene symbol matching
cellNames | IterableFragments methods
cellNames<- | IterableFragments methods
checksum | Calculate the MD5 checksum of an IterableMatrix
chrNames | IterableFragments methods
chrNames<- | IterableFragments methods
cluster_graph_leiden | Cluster an adjacency matrix
cluster_graph_louvain | Cluster an adjacency matrix
cluster_graph_seurat | Cluster an adjacency matrix
cluster_membership_matrix | Convert grouping vector to sparse matrix
collect_features | Collect features for plotting
colMaxs | IterableMatrix methods
colMeans-method | IterableMatrix methods
colQuantiles | IterableMatrix methods
colSums-method | IterableMatrix methods
colVars | IterableMatrix methods
continuous_palette | Color palettes
convert_matrix_type | Convert the type of a matrix
convert_to_fragments | Convert between BPCells fragments and R objects.

## -- D --

discrete_palette | Color palettes

## -- E --

expm1-method | IterableMatrix methods
expm1_slow | IterableMatrix methods
extend_ranges | Extend genome ranges in a strand-aware fashion.

## -- F --

footprint | Get footprints around a set of genomic coordinates
fragments_identical | Check if two fragments objects are identical

## -- G --

gene_region | Find gene region
gene_score_archr | Calculate GeneActivityScores
gene_score_tiles_archr | Calculate gene-tile distances for ArchR gene activities
gene_score_weights_archr | Calculate GeneActivityScores
genomic-ranges-like | Genomic range formats
get_trackplot_height | Adjust trackplot properties

## -- H --

human_gene_mapping | Gene Symbol Mapping data

## -- I --

import_matrix_market | Import MatrixMarket files
import_matrix_market_10x | Import MatrixMarket files
IterableFragments-methods | IterableFragments methods
IterableMatrix-methods | IterableMatrix methods

## -- K --

knn_annoy | Get a knn matrix from reduced dimensions
knn_hnsw | Get a knn matrix from reduced dimensions
knn_to_geodesic_graph | K Nearest Neighbor (KNN) Graph
knn_to_graph | K Nearest Neighbor (KNN) Graph
knn_to_snn_graph | K Nearest Neighbor (KNN) Graph

## -- L --

log1p-method | IterableMatrix methods
log1p_slow | IterableMatrix methods

## -- M --

marker_features | Test for marker features
match_gene_symbol | Gene symbol matching
matrix_R_conversion | Convert between BPCells matrix and R objects.
matrix_stats | Calculate matrix stats
matrix_type | IterableMatrix methods
merge_cells | Merge cells into pseudobulks
merge_peaks_iterative | Merge peaks
min_by_col | Elementwise minimum
min_by_row | Elementwise minimum
min_scalar | Elementwise minimum
mouse_gene_mapping | Gene Symbol Mapping data
multiply_cols | Broadcasting vector arithmetic
multiply_rows | Broadcasting vector arithmetic

## -- N --

normalize_ranges | Normalize an object representing genomic ranges
nucleosome_counts | Count fragments by nucleosomal size

## -- O --

open_fragments_10x | Read/write a 10x fragments file
open_fragments_dir | Read/write BPCells fragment objects
open_fragments_hdf5 | Read/write BPCells fragment objects
open_matrix_10x_hdf5 | Read/write a 10x feature matrix
open_matrix_anndata_hdf5 | Read/write AnnData matrix
open_matrix_dir | Read/write sparse matrices
open_matrix_hdf5 | Read/write sparse matrices
order_ranges | Get end-sorted ordering for genome ranges

## -- P --

peak_matrix | Calculate ranges x cells overlap matrix
plot_dot | Dotplot
plot_embedding | Plot UMAP or embeddings
plot_fragment_length | Fragment size distribution
plot_read_count_knee | Knee plot of single cell read counts
plot_tf_footprint | Plot TF footprint
plot_tss_profile | Plot TSS profile
plot_tss_scatter | TSS Enrichment vs. Fragment Counts plot
prefix_cell_names | Add sample prefix to cell names
pseudobulk_matrix | Aggregate counts matrices by cell group or feature.

## -- Q --

qc_scATAC | Calculate ArchR-compatible per-cell QC statistics

## -- R --

range_distance_to_nearest | Find signed distance to nearest genomic ranges
read_bed | Read a bed file into a data frame
read_encode_blacklist | Read a bed file into a data frame
read_gencode_genes | Read GTF gene annotations
read_gencode_transcripts | Read GTF gene annotations
read_gtf | Read GTF gene annotations
read_ucsc_chrom_sizes | Read UCSC chromosome sizes
regress_out | Regress out unwanted variation
rotate_x_labels | Rotate ggplot x axis labels
round-method | IterableMatrix methods
rowMaxs | IterableMatrix methods
rowMeans-method | IterableMatrix methods
rowQuantiles | IterableMatrix methods
rowSums-method | IterableMatrix methods
rowVars | IterableMatrix methods

## -- S --

sctransform_pearson | SCTransform Pearson Residuals
select_cells | Subset, translate, or reorder cell IDs
select_chromosomes | Subset, translate, or reorder chromosome IDs
select_regions | Subset fragments by genomic region
set_trackplot_height | Adjust trackplot properties
set_trackplot_label | Adjust trackplot properties
shift_fragments | Shift start or end coordinates
show-method | IterableFragments methods
show-method | IterableMatrix methods
storage_order | IterableMatrix methods
subset_lengths | Subset fragments by length
svds | Calculate svds

## -- T --

t-method | IterableMatrix methods
tile_matrix | Calculate ranges x cells tile overlap matrix
trackplot_combine | Combine track plots
trackplot_coverage | Pseudobulk coverage trackplot
trackplot_gene | Plot transcript models
trackplot_genome_annotation | Plot range-based annotation tracks (e.g. peaks)
trackplot_loop | Plot loops
trackplot_scalebar | Plot scale bar
transpose_storage_order | Transpose the storage order for a matrix

## -- W --

write_fragments_10x | Read/write a 10x fragments file
write_fragments_dir | Read/write BPCells fragment objects
write_fragments_hdf5 | Read/write BPCells fragment objects
write_fragments_memory | Read/write BPCells fragment objects
write_insertion_bedgraph | Write insertion counts to bedgraph file
write_matrix_10x_hdf5 | Read/write a 10x feature matrix
write_matrix_anndata_hdf5 | Read/write AnnData matrix
write_matrix_dir | Read/write sparse matrices
write_matrix_hdf5 | Read/write sparse matrices
write_matrix_memory | Read/write sparse matrices

## -- misc --

%*%-method | IterableMatrix methods
*-method | IterableMatrix methods
+-method | IterableMatrix methods
--method | IterableMatrix methods
/-method | IterableMatrix methods
<-method | IterableMatrix methods
<=-method | IterableMatrix methods
>-method | IterableMatrix methods
>=-method | IterableMatrix methods
^-method | IterableMatrix methods