Package index
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open_fragments_10x()
write_fragments_10x()
- Read/write a 10x fragments file
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write_fragments_memory()
write_fragments_dir()
open_fragments_dir()
write_fragments_hdf5()
open_fragments_hdf5()
- Read/write BPCells fragment objects
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convert_to_fragments()
as()
as.data.frame()
- Convert between BPCells fragments and R objects.
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qc_scATAC()
- Calculate ArchR-compatible per-cell QC statistics
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nucleosome_counts()
- Count fragments by nucleosomal size
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footprint()
- Get footprints around a set of genomic coordinates
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peak_matrix()
- Calculate ranges x cells overlap matrix
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tile_matrix()
- Calculate ranges x cells tile overlap matrix
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gene_score_weights_archr()
gene_score_archr()
- Calculate GeneActivityScores
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call_peaks_tile()
- Call peaks from tiles
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merge_peaks_iterative()
- Merge peaks
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write_insertion_bedgraph()
- Write insertion counts to bedgraph file
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shift_fragments()
- Shift start or end coordinates
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select_chromosomes()
- Subset, translate, or reorder chromosome IDs
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select_cells()
- Subset, translate, or reorder cell IDs
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merge_cells()
- Merge cells into pseudobulks
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subset_lengths()
- Subset fragments by length
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select_regions()
- Subset fragments by genomic region
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prefix_cell_names()
- Add sample prefix to cell names
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show(<IterableFragments>)
cellNames()
`cellNames<-`()
chrNames()
`chrNames<-`()
- IterableFragments methods
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fragments_identical()
- Check if two fragments objects are identical
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genomic-ranges-like
- Genomic range formats
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order_ranges()
- Get end-sorted ordering for genome ranges
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range_distance_to_nearest()
- Find signed distance to nearest genomic ranges
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extend_ranges()
- Extend genome ranges in a strand-aware fashion.
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gene_score_tiles_archr()
- Calculate gene-tile distances for ArchR gene activities
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normalize_ranges()
- Normalize an object representing genomic ranges
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open_matrix_10x_hdf5()
write_matrix_10x_hdf5()
- Read/write a 10x feature matrix
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open_matrix_anndata_hdf5()
write_matrix_anndata_hdf5()
- Read/write AnnData matrix
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write_matrix_memory()
write_matrix_dir()
open_matrix_dir()
write_matrix_hdf5()
open_matrix_hdf5()
- Read/write sparse matrices
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import_matrix_market()
import_matrix_market_10x()
- Import MatrixMarket files
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as()
as.matrix()
- Convert between BPCells matrix and R objects.
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marker_features()
- Test for marker features
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matrix_stats()
- Calculate matrix stats
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svds()
- Calculate svds
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convert_matrix_type()
- Convert the type of a matrix
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transpose_storage_order()
- Transpose the storage order for a matrix
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sctransform_pearson()
- SCTransform Pearson Residuals
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min_scalar()
min_by_row()
min_by_col()
- Elementwise minimum
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add_rows()
add_cols()
multiply_rows()
multiply_cols()
- Broadcasting vector arithmetic
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binarize()
- Convert matrix elements to zeros and ones
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all_matrix_inputs()
`all_matrix_inputs<-`()
- Get/set inputs to a matrix transform
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checksum()
- Calculate the MD5 checksum of an IterableMatrix
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apply_by_row()
apply_by_col()
- Apply a function to summarize rows/cols
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regress_out()
- Regress out unwanted variation
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matrix_type()
storage_order()
show(<IterableMatrix>)
t(<IterableMatrix>)
`%*%`(<IterableMatrix>,<matrix>)
rowSums(<IterableMatrix>)
colSums(<IterableMatrix>)
rowMeans(<IterableMatrix>)
colMeans(<IterableMatrix>)
colVars()
rowVars()
rowMaxs()
colMaxs()
log1p(<IterableMatrix>)
log1p_slow()
expm1(<IterableMatrix>)
expm1_slow()
`^`(<IterableMatrix>,<numeric>)
`<`(<numeric>,<IterableMatrix>)
`>`(<IterableMatrix>,<numeric>)
`<=`(<numeric>,<IterableMatrix>)
`>=`(<IterableMatrix>,<numeric>)
round(<IterableMatrix>)
`*`(<IterableMatrix>,<numeric>)
`+`(<IterableMatrix>,<numeric>)
`/`(<IterableMatrix>,<numeric>)
`-`(<IterableMatrix>,<numeric>)
- IterableMatrix methods
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human_gene_mapping
mouse_gene_mapping
- Gene Symbol Mapping data
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match_gene_symbol()
canonical_gene_symbol()
- Gene symbol matching
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read_gtf()
read_gencode_genes()
read_gencode_transcripts()
- Read GTF gene annotations
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read_bed()
read_encode_blacklist()
- Read a bed file into a data frame
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read_ucsc_chrom_sizes()
- Read UCSC chromosome sizes
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knn_hnsw()
knn_annoy()
- Get a knn matrix from reduced dimensions
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cluster_graph_leiden()
cluster_graph_louvain()
cluster_graph_seurat()
- Cluster an adjacency matrix
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knn_to_graph()
knn_to_snn_graph()
knn_to_geodesic_graph()
- K Nearest Neighbor (KNN) Graph
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cluster_membership_matrix()
- Convert grouping vector to sparse matrix
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plot_read_count_knee()
- Knee plot of single cell read counts
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plot_embedding()
- Plot UMAP or embeddings
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plot_dot()
- Dotplot
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plot_fragment_length()
- Fragment size distribution
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plot_tf_footprint()
- Plot TF footprint
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plot_tss_profile()
- Plot TSS profile
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plot_tss_scatter()
- TSS Enrichment vs. Fragment Counts plot
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trackplot_combine()
- Combine track plots
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trackplot_coverage()
- Pseudobulk coverage trackplot
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trackplot_gene()
- Plot transcript models
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trackplot_loop()
- Plot loops
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trackplot_genome_annotation()
- Plot range-based annotation tracks (e.g. peaks)
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trackplot_scalebar()
- Plot scale bar
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gene_region()
- Find gene region
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set_trackplot_label()
set_trackplot_height()
get_trackplot_height()
- Adjust trackplot properties
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discrete_palette()
continuous_palette()
- Color palettes
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collect_features()
- Collect features for plotting
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rotate_x_labels()
- Rotate ggplot x axis labels