%*%,IterableMatrix,matrix-method	IterableMatrix-methods
%>%	reexports
*,IterableMatrix,numeric-method	IterableMatrix-methods
+,IterableMatrix,numeric-method	IterableMatrix-methods
-,IterableMatrix,numeric-method	IterableMatrix-methods
/,IterableMatrix,numeric-method	IterableMatrix-methods
<,numeric,IterableMatrix-method	IterableMatrix-methods
<=,numeric,IterableMatrix-method	IterableMatrix-methods
>,IterableMatrix,numeric-method	IterableMatrix-methods
>=,IterableMatrix,numeric-method	IterableMatrix-methods
add_cols	mat_norm
add_rows	mat_norm
all_matrix_inputs	all_matrix_inputs
all_matrix_inputs<-	all_matrix_inputs
apply_by_col	apply_by_row
apply_by_row	apply_by_row
binarize	binarize
call_macs_peaks	call_macs_peaks
call_peaks_macs	call_peaks_macs
call_peaks_tile	call_peaks_tile
canonical_gene_symbol	gene_matching
cellNames	IterableFragments-methods
cellNames<-	IterableFragments-methods
checksum	checksum
chrNames	IterableFragments-methods
chrNames<-	IterableFragments-methods
cluster_graph_leiden	cluster
cluster_graph_louvain	cluster
cluster_graph_seurat	cluster
cluster_membership_matrix	cluster_membership_matrix
collect_features	collect_features
colMaxs	IterableMatrix-methods
colMeans	reexports
colMeans,IterableMatrix-method	IterableMatrix-methods
colQuantiles	IterableMatrix-methods
colSums	reexports
colSums,IterableMatrix-method	IterableMatrix-methods
colVars	IterableMatrix-methods
concat_dimnames	concat_dimnames
continuous_palette	palettes
convert_matrix_type	convert_matrix_type
convert_to_fragments	fragment_R_conversion
discrete_palette	palettes
draw_trackplot_grid	draw_trackplot_grid
ensure_downloaded	ensure_downloaded
EXPERIMENTAL_open_matrix_dir	EXPERIMENTAL_open_matrix_dir
EXPERIMENTAL_write_matrix_dir	EXPERIMENTAL_write_matrix_dir
expm1,IterableMatrix-method	IterableMatrix-methods
expm1_slow	IterableMatrix-methods
extend_ranges	extend_ranges
footprint	footprint
fragments_identical	fragments_identical
gene_region	gene_region
gene_score_archr	gene_scores
gene_score_tiles_archr	gene_score_tiles_archr
gene_score_weights_archr	gene_scores
genomic-ranges-like	genomic-ranges-like
get_demo_frags	demo_data
get_demo_mat	demo_data
get_trackplot_height	trackplot_utils
human_gene_mapping	gene_mapping
import_matrix_market	import_matrix_market
import_matrix_market_10x	import_matrix_market
IterableFragments-methods	IterableFragments-methods
IterableMatrix-methods	IterableMatrix-methods
iterate_matrix	iterate_matrix
knn_annoy	knn
knn_hnsw	knn
knn_to_geodesic_graph	knn_graph
knn_to_graph	knn_graph
knn_to_snn_graph	knn_graph
LinearOperator-class	LinearOperator-class
linear_operator	linear_operator
log1p,IterableMatrix-method	IterableMatrix-methods
log1p_slow	IterableMatrix-methods
macs_path_is_valid	macs_path_is_valid
marker_features	marker_features
mask_matrix	mask_matrix
match_gene_symbol	gene_matching
matrix_inputs	matrix_inputs
matrix_R_conversion	matrix_R_conversion
matrix_stats	matrix_stats
matrix_type	IterableMatrix-methods
merge_cells	merge_cells
merge_dimnames	merge_dimnames
merge_peaks_iterative	merge_peaks_iterative
min_by_col	min_elementwise
min_by_row	min_elementwise
min_scalar	min_elementwise
mouse_gene_mapping	gene_mapping
multiply_cols	mat_norm
multiply_rows	mat_norm
normalized_dimnames	normalized_dimnames
normalize_ranges	normalize_ranges
normalize_unique_file_names	normalize_unique_file_names
nucleosome_counts	nucleosome_counts
open_fragments_10x	open_fragments_10x
open_fragments_dir	fragment_io
open_fragments_hdf5	fragment_io
open_matrix_10x_hdf5	open_matrix_10x_hdf5
open_matrix_anndata_hdf5	open_matrix_anndata_hdf5
open_matrix_dir	matrix_io
open_matrix_hdf5	matrix_io
order_ranges	order_ranges
parallel_split	parallel_split
peak_matrix	peak_matrix
plot_dot	plot_dot
plot_embedding	plot_embedding
plot_fragment_length	plot_fragment_length
plot_read_count_knee	plot_read_count_knee
plot_tf_footprint	plot_tf_footprint
plot_tss_profile	plot_tss_profile
plot_tss_scatter	plot_tss_scatter
prefix_cell_names	prefix_cell_names
prepare_demo_data	prepare_demo_data
pseudobulk_matrix	pseudobulk_matrix
qc_scATAC	qc_scATAC
range_distance_to_nearest	range_distance_to_nearest
rank_transform	rank_transform
read_bed	read_bed
read_encode_blacklist	read_bed
read_gencode_genes	read_gtf
read_gencode_transcripts	read_gtf
read_gtf	read_gtf
read_ucsc_chrom_sizes	read_ucsc_chrom_sizes
reexports	reexports
regress_out	regress_out
remove_demo_data	demo_data
render_plot_from_storage	render_plot_from_storage
rotate_x_labels	rotate_x_labels
round,IterableMatrix-method	IterableMatrix-methods
rowMaxs	IterableMatrix-methods
rowMeans	reexports
rowMeans,IterableMatrix-method	IterableMatrix-methods
rowQuantiles	IterableMatrix-methods
rowSums	reexports
rowSums,IterableMatrix-method	IterableMatrix-methods
rowVars	IterableMatrix-methods
scan_fragments	scan_fragments
sctransform_pearson	sctransform_pearson
select_cells	select_cells
select_chromosomes	select_chromosomes
select_regions	select_regions
set_threads	set_threads
set_trackplot_height	trackplot_utils
set_trackplot_label	trackplot_utils
shift_fragments	shift_fragments
show,IterableFragments-method	IterableFragments-methods
show,IterableMatrix-method	IterableMatrix-methods
storage_order	IterableMatrix-methods
subset_lengths	subset_lengths
svds	svds
t,IterableMatrix-method	IterableMatrix-methods
tile_matrix	tile_matrix
tile_ranges	tile_ranges
trackplot_bulk	trackplot_bulk
trackplot_calculate_segment_height	trackplot_calculate_segment_height
trackplot_combine	trackplot_combine
trackplot_coverage	trackplot_coverage
trackplot_create_arrow_segs	trackplot_create_arrow_segs
trackplot_gene	trackplot_gene
trackplot_genome_annotation	trackplot_genome_annotation
trackplot_loop	trackplot_loop
trackplot_normalize_ranges_with_metadata	trackplot_normalize_ranges_with_metadata
trackplot_scalebar	trackplot_scalebar
transpose_storage_order	transpose_storage_order
wrapMatrix	wrapMatrix
write_fragments_10x	open_fragments_10x
write_fragments_dir	fragment_io
write_fragments_hdf5	fragment_io
write_fragments_memory	fragment_io
write_insertion_bed	write_insertion_bed
write_insertion_bedgraph	write_insertion_bedgraph
write_matrix_10x_hdf5	open_matrix_10x_hdf5
write_matrix_anndata_hdf5	open_matrix_anndata_hdf5
write_matrix_anndata_hdf5_dense	open_matrix_anndata_hdf5
write_matrix_dir	matrix_io
write_matrix_hdf5	matrix_io
write_matrix_memory	matrix_io
^,IterableMatrix,numeric-method	IterableMatrix-methods
