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ATAC-seq Fragments

Fragment I/O

open_fragments_10x() write_fragments_10x()
Read/write a 10x fragments file
write_fragments_memory() write_fragments_dir() open_fragments_dir() write_fragments_hdf5() open_fragments_hdf5()
Read/write BPCells fragment objects
convert_to_fragments() as() as.data.frame()
Convert between BPCells fragments and R objects.

ATAC Analysis

qc_scATAC()
Calculate ArchR-compatible per-cell QC statistics
nucleosome_counts()
Count fragments by nucleosomal size
footprint()
Get footprints around a set of genomic coordinates
peak_matrix()
Calculate ranges x cells overlap matrix
tile_matrix()
Calculate ranges x cells tile overlap matrix
gene_score_weights_archr() gene_score_archr()
Calculate GeneActivityScores
call_peaks_tile()
Call peaks from tiles
merge_peaks_iterative()
Merge peaks
write_insertion_bedgraph()
Write insertion counts to bedgraph file

Fragment Operations

shift_fragments()
Shift start or end coordinates
select_chromosomes()
Subset, translate, or reorder chromosome IDs
select_cells()
Subset, translate, or reorder cell IDs
merge_cells()
Merge cells into pseudobulks
subset_lengths()
Subset fragments by length
select_regions()
Subset fragments by genomic region
prefix_cell_names()
Add sample prefix to cell names
show(<IterableFragments>) cellNames() `cellNames<-`() chrNames() `chrNames<-`()
IterableFragments methods
fragments_identical()
Check if two fragments objects are identical

Genomic Range Calculations

genomic-ranges-like
Genomic range formats
order_ranges()
Get end-sorted ordering for genome ranges
range_distance_to_nearest()
Find signed distance to nearest genomic ranges
extend_ranges()
Extend genome ranges in a strand-aware fashion.
gene_score_tiles_archr()
Calculate gene-tile distances for ArchR gene activities
normalize_ranges()
Normalize an object representing genomic ranges

Matrix Operations (RNA + ATAC)

Matrix I/O

open_matrix_10x_hdf5() write_matrix_10x_hdf5()
Read/write a 10x feature matrix
open_matrix_anndata_hdf5() write_matrix_anndata_hdf5()
Read/write AnnData matrix
write_matrix_memory() write_matrix_dir() open_matrix_dir() write_matrix_hdf5() open_matrix_hdf5()
Read/write sparse matrices
import_matrix_market() import_matrix_market_10x()
Import MatrixMarket files
as() as.matrix()
Convert between BPCells matrix and R objects.

Matrix Operations

Reference Annotations

human_gene_mapping mouse_gene_mapping
Gene Symbol Mapping data
match_gene_symbol() canonical_gene_symbol()
Gene symbol matching
read_gtf() read_gencode_genes() read_gencode_transcripts()
Read GTF gene annotations
read_bed() read_encode_blacklist()
Read a bed file into a data frame
read_ucsc_chrom_sizes()
Read UCSC chromosome sizes

Clustering

knn_hnsw() knn_annoy()
Get a knn matrix from reduced dimensions
cluster_graph_leiden() cluster_graph_louvain() cluster_graph_seurat()
Cluster an adjacency matrix
knn_to_graph() knn_to_snn_graph() knn_to_geodesic_graph()
K Nearest Neighbor (KNN) Graph
cluster_membership_matrix()
Convert grouping vector to sparse matrix

Plots

Single cell plots

plot_read_count_knee()
Knee plot of single cell read counts
plot_embedding()
Plot UMAP or embeddings
plot_dot()
Dotplot
plot_fragment_length()
Fragment size distribution
plot_tf_footprint()
Plot TF footprint
plot_tss_profile()
Plot TSS profile
plot_tss_scatter()
TSS Enrichment vs. Fragment Counts plot

Genomic track plots

trackplot_combine()
Combine track plots
trackplot_coverage()
Pseudobulk coverage trackplot
trackplot_gene()
Plot transcript models
trackplot_loop()
Plot loops
trackplot_genome_annotation()
Plot range-based annotation tracks (e.g. peaks)
trackplot_scalebar()
Plot scale bar
gene_region()
Find gene region
set_trackplot_label() set_trackplot_height() get_trackplot_height()
Adjust trackplot properties

Plotting utilities

discrete_palette() continuous_palette()
Color palettes
collect_features()
Collect features for plotting
rotate_x_labels()
Rotate ggplot x axis labels