add_rows                Broadcasting vector arithmetic
all_matrix_inputs       Get/set inputs to a matrix transform
apply_by_row            Apply a function to summarize rows/cols
binarize                Convert matrix elements to zeros and ones
call_peaks_macs         Call peaks using MACS2/3
call_peaks_tile         Call peaks from tiles
checksum                Calculate the MD5 checksum of an IterableMatrix
cluster_graph_leiden    Cluster an adjacency matrix
cluster_membership_matrix
                        Convert grouping vector to sparse matrix
collect_features        Collect features for plotting
convert_matrix_type     Convert the type of a matrix
convert_to_fragments    Convert between BPCells fragments and R
                        objects.
discrete_palette        Color palettes
extend_ranges           Extend genome ranges in a strand-aware fashion.
footprint               Get footprints around a set of genomic
                        coordinates
fragments_identical     Check if two fragments objects are identical
gene_region             Find gene region
gene_score_tiles_archr
                        Calculate gene-tile distances for ArchR gene
                        activities
gene_score_weights_archr
                        Calculate GeneActivityScores
genomic-ranges-like     Genomic range formats
human_gene_mapping      Gene Symbol Mapping data
import_matrix_market    Import MatrixMarket files
IterableFragments-methods
                        IterableFragments methods
IterableMatrix-methods
                        IterableMatrix methods
knn_hnsw                Get a knn matrix from reduced dimensions
knn_to_graph            K Nearest Neighbor (KNN) Graph
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
merge_cells             Merge cells into pseudobulks
merge_peaks_iterative   Merge peaks
min_scalar              Elementwise minimum
normalize_ranges        Normalize an object representing genomic ranges
nucleosome_counts       Count fragments by nucleosomal size
open_fragments_10x      Read/write a 10x fragments file
open_matrix_10x_hdf5    Read/write a 10x feature matrix
open_matrix_anndata_hdf5
                        Read/write AnnData matrix
order_ranges            Get end-sorted ordering for genome ranges
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.
qc_scATAC               Calculate ArchR-compatible per-cell QC
                        statistics
range_distance_to_nearest
                        Find signed distance to nearest genomic ranges
read_bed                Read a bed file into a data frame
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
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_label     Adjust trackplot properties
shift_fragments         Shift start or end coordinates
subset_lengths          Subset fragments by length
svds                    Calculate svds
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
write_fragments_memory
                        Read/write BPCells fragment objects
write_insertion_bedgraph
                        Write insertion counts to bedgraph file
write_matrix_memory     Read/write sparse matrices
