Package: BPCells 0.1.0

Benjamin Parks

BPCells: Single Cell Counts Matrices to PCA

> Efficient operations for single cell ATAC-seq fragments and RNA counts matrices. Interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.

Authors:Benjamin Parks [aut, cre]

BPCells_0.1.0.tar.gz
BPCells_0.1.0.zip(r-4.5)BPCells_0.1.0.zip(r-4.4)BPCells_0.1.0.zip(r-4.3)
BPCells_0.1.0.tgz(r-4.4-arm64)BPCells_0.1.0.tgz(r-4.4-x86_64)BPCells_0.1.0.tgz(r-4.3-arm64)BPCells_0.1.0.tgz(r-4.3-x86_64)
BPCells_0.1.0.tar.gz(r-4.5-noble)BPCells_0.1.0.tar.gz(r-4.4-noble)
BPCells.pdf |BPCells.html
BPCells/json (API)
NEWS

# Install 'BPCells' in R:
install.packages('BPCells', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bnprks/bpcells/issues

Uses libs:
  • zlib– Compression library
  • hdf5– HDF5 C runtime files - serial version
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

108 exports 133 stars 4.91 score 42 dependencies

Last updated 2 months agofrom:b96a44048d

Exports:add_colsadd_rowsall_matrix_inputsall_matrix_inputs<-as.data.frameas.matrixbinarizecall_peaks_tilecanonical_gene_symbolcellNamescellNames<-checksumchrNameschrNames<-cluster_graph_leidencluster_graph_louvaincluster_graph_seuratcollect_featurescolMeanscolSumscontinuous_paletteconvert_matrix_typeconvert_to_fragmentsdiscrete_palettedraw_trackplot_gridexpm1_slowextend_rangesfootprintgene_regiongene_score_archrgene_score_tiles_archrgene_score_weights_archrget_trackplot_heightimport_matrix_marketimport_matrix_market_10xknn_annoyknn_hnswknn_to_geodesic_graphknn_to_snn_graphlog1p_slowmarker_featuresmatch_gene_symbolmatrix_statsmatrix_typemerge_cellsmin_by_colmin_by_rowmin_scalarmultiply_colsmultiply_rowsnucleosome_countsopen_fragments_10xopen_fragments_diropen_fragments_hdf5open_matrix_10x_hdf5open_matrix_anndata_hdf5open_matrix_diropen_matrix_hdf5order_rangespeak_matrixplot_dotplot_embeddingplot_fragment_lengthplot_read_count_kneeplot_tf_footprintplot_tss_profileplot_tss_scatterpow_slowprefix_cell_namesqc_scATACrange_distance_to_nearestread_bedread_encode_blacklistread_gencode_genesread_gencode_transcriptsread_gtfread_ucsc_chrom_sizesrotate_x_labelsrowMeansrowSumssctransform_pearsonselect_cellsselect_chromosomesselect_regionsset_trackplot_heightset_trackplot_labelshift_fragmentsstorage_ordersubset_lengthssvdsttile_matrixtrackplot_bulktrackplot_combinetrackplot_coveragetrackplot_genetrackplot_looptrackplot_scalebartranspose_storage_orderwrite_fragments_10xwrite_fragments_dirwrite_fragments_hdf5write_fragments_memorywrite_matrix_10x_hdf5write_matrix_anndata_hdf5write_matrix_dirwrite_matrix_hdf5write_matrix_memory

Dependencies:clicolorspacecpp11dplyrfansifarvergenericsggplot2ggrepelgluegtablehexbinisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepatchworkpillarpkgconfigpurrrR6RColorBrewerRcppRcppEigenrlangscalesscattermorestringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Broadcasting vector arithmeticadd_cols add_rows multiply_cols multiply_rows
Get/set inputs to a matrix transformall_matrix_inputs all_matrix_inputs<-
Convert matrix elements to zeros and onesbinarize
Call peaks from tilescall_peaks_tile
Calculate the MD5 checksum of an IterableMatrixchecksum
Cluster an adjacency matrixcluster_graph_leiden cluster_graph_louvain cluster_graph_seurat
Convert grouping vector to sparse matrixcluster_membership_matrix
Collect features for plottingcollect_features
Convert the type of a matrixconvert_matrix_type
Convert between BPCells fragments and R objects.convert_to_fragments
Color palettescontinuous_palette discrete_palette
Extend genome ranges in a strand-aware fashion.extend_ranges
Get footprints around a set of genomic coordinatesfootprint
Check if two fragments objects are identicalfragments_identical
Find gene regiongene_region
Calculate gene-tile distances for ArchR gene activitiesgene_score_tiles_archr
Calculate GeneActivityScoresgene_score_archr gene_score_weights_archr
Genomic range formatsgenomic-ranges-like
Gene Symbol Mapping datahuman_gene_mapping mouse_gene_mapping
Import MatrixMarket filesimport_matrix_market import_matrix_market_10x
IterableFragments methodscellNames cellNames<- chrNames chrNames<- IterableFragments-methods show,IterableFragments-method
IterableMatrix methods%*%,IterableMatrix,matrix-method *,IterableMatrix,numeric-method +,IterableMatrix,numeric-method -,IterableMatrix,numeric-method /,IterableMatrix,numeric-method <,numeric,IterableMatrix-method <=,numeric,IterableMatrix-method >,IterableMatrix,numeric-method >=,IterableMatrix,numeric-method colMeans,IterableMatrix-method colSums,IterableMatrix-method expm1,IterableMatrix-method expm1_slow IterableMatrix-methods log1p,IterableMatrix-method log1p_slow matrix_type pow_slow round,IterableMatrix-method rowMeans,IterableMatrix-method rowSums,IterableMatrix-method show,IterableMatrix-method storage_order t,IterableMatrix-method ^,IterableMatrix,numeric-method
Get a knn matrix from reduced dimensionsknn_annoy knn_hnsw
K Nearest Neighbor (KNN) Graphknn_to_geodesic_graph knn_to_graph knn_to_snn_graph
Test for marker featuresmarker_features
Gene symbol matchingcanonical_gene_symbol match_gene_symbol
Convert between BPCells matrix and R objects.matrix_R_conversion
Calculate matrix statsmatrix_stats
Merge cells into pseudobulksmerge_cells
Merge peaksmerge_peaks_iterative
Elementwise minimummin_by_col min_by_row min_scalar
Normalize an object representing genomic rangesnormalize_ranges
Count fragments by nucleosomal sizenucleosome_counts
Read/write a 10x fragments fileopen_fragments_10x write_fragments_10x
Read/write a 10x feature matrixopen_matrix_10x_hdf5 write_matrix_10x_hdf5
Read/write AnnData matrixopen_matrix_anndata_hdf5 write_matrix_anndata_hdf5
Get end-sorted ordering for genome rangesorder_ranges
Calculate ranges x cells overlap matrixpeak_matrix
Dotplotplot_dot
Plot UMAP or embeddingsplot_embedding
Fragment size distributionplot_fragment_length
Knee plot of single cell read countsplot_read_count_knee
Plot TF footprintplot_tf_footprint
Plot TSS profileplot_tss_profile
TSS Enrichment vs. Fragment Counts plotplot_tss_scatter
Add sample prefix to cell namesprefix_cell_names
Calculate ArchR-compatible per-cell QC statisticsqc_scATAC
Find signed distance to nearest genomic rangesrange_distance_to_nearest
Read a bed file into a data frameread_bed read_encode_blacklist
Read GTF gene annotationsread_gencode_genes read_gencode_transcripts read_gtf
Read UCSC chromosome sizesread_ucsc_chrom_sizes
Rotate ggplot x axis labelsrotate_x_labels
SCTransform Pearson Residualssctransform_pearson
Subset, translate, or reorder cell IDsselect_cells
Subset, translate, or reorder chromosome IDsselect_chromosomes
Subset fragments by genomic regionselect_regions
Adjust trackplot propertiesget_trackplot_height set_trackplot_height set_trackplot_label
Shift start or end coordinatesshift_fragments
Subset fragments by lengthsubset_lengths
Calculate svdssvds
Calculate ranges x cells tile overlap matrixtile_matrix
Combine track plotstrackplot_combine
Pseudobulk coverage trackplottrackplot_coverage
Plot transcript modelstrackplot_gene
Plot loopstrackplot_loop
Plot scale bartrackplot_scalebar
Transpose the storage order for a matrixtranspose_storage_order
Read/write BPCells fragment objectsopen_fragments_dir open_fragments_hdf5 write_fragments_dir write_fragments_hdf5 write_fragments_memory
Read/write sparse matricesopen_matrix_dir open_matrix_hdf5 write_matrix_dir write_matrix_hdf5 write_matrix_memory