Package: BPCells 0.1.0
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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:
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-x86_64)BPCells_0.1.0.tgz(r-4.4-arm64)BPCells_0.1.0.tgz(r-4.3-x86_64)BPCells_0.1.0.tgz(r-4.3-arm64)
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')) |
Bug tracker:https://github.com/bnprks/bpcells/issues
- human_gene_mapping - Gene Symbol Mapping data
- mouse_gene_mapping - Gene Symbol Mapping data
Last updated 3 months agofrom:b96a44048d. Checks:OK: 1 WARNING: 8. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 29 2024 |
R-4.5-win-x86_64 | WARNING | Aug 29 2024 |
R-4.5-linux-x86_64 | WARNING | Aug 29 2024 |
R-4.4-win-x86_64 | WARNING | Aug 29 2024 |
R-4.4-mac-x86_64 | WARNING | Aug 29 2024 |
R-4.4-mac-aarch64 | WARNING | Aug 29 2024 |
R-4.3-win-x86_64 | WARNING | Aug 29 2024 |
R-4.3-mac-x86_64 | WARNING | Aug 29 2024 |
R-4.3-mac-aarch64 | WARNING | Aug 29 2024 |
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 page | Topics |
---|---|
Broadcasting vector arithmetic | add_cols add_rows multiply_cols multiply_rows |
Get/set inputs to a matrix transform | all_matrix_inputs all_matrix_inputs<- |
Convert matrix elements to zeros and ones | binarize |
Call peaks from tiles | call_peaks_tile |
Calculate the MD5 checksum of an IterableMatrix | checksum |
Cluster an adjacency matrix | cluster_graph_leiden cluster_graph_louvain cluster_graph_seurat |
Convert grouping vector to sparse matrix | cluster_membership_matrix |
Collect features for plotting | collect_features |
Convert the type of a matrix | convert_matrix_type |
Convert between BPCells fragments and R objects. | convert_to_fragments |
Color palettes | continuous_palette discrete_palette |
Extend genome ranges in a strand-aware fashion. | extend_ranges |
Get footprints around a set of genomic coordinates | footprint |
Check if two fragments objects are identical | fragments_identical |
Find gene region | gene_region |
Calculate gene-tile distances for ArchR gene activities | gene_score_tiles_archr |
Calculate GeneActivityScores | gene_score_archr gene_score_weights_archr |
Genomic range formats | genomic-ranges-like |
Gene Symbol Mapping data | human_gene_mapping mouse_gene_mapping |
Import MatrixMarket files | import_matrix_market import_matrix_market_10x |
IterableFragments methods | cellNames 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 dimensions | knn_annoy knn_hnsw |
K Nearest Neighbor (KNN) Graph | knn_to_geodesic_graph knn_to_graph knn_to_snn_graph |
Test for marker features | marker_features |
Gene symbol matching | canonical_gene_symbol match_gene_symbol |
Convert between BPCells matrix and R objects. | matrix_R_conversion |
Calculate matrix stats | matrix_stats |
Merge cells into pseudobulks | merge_cells |
Merge peaks | merge_peaks_iterative |
Elementwise minimum | min_by_col min_by_row min_scalar |
Normalize an object representing genomic ranges | normalize_ranges |
Count fragments by nucleosomal size | nucleosome_counts |
Read/write a 10x fragments file | open_fragments_10x write_fragments_10x |
Read/write a 10x feature matrix | open_matrix_10x_hdf5 write_matrix_10x_hdf5 |
Read/write AnnData matrix | open_matrix_anndata_hdf5 write_matrix_anndata_hdf5 |
Get end-sorted ordering for genome ranges | order_ranges |
Calculate ranges x cells overlap matrix | peak_matrix |
Dotplot | plot_dot |
Plot UMAP or embeddings | plot_embedding |
Fragment size distribution | plot_fragment_length |
Knee plot of single cell read counts | plot_read_count_knee |
Plot TF footprint | plot_tf_footprint |
Plot TSS profile | plot_tss_profile |
TSS Enrichment vs. Fragment Counts plot | plot_tss_scatter |
Add sample prefix to cell names | prefix_cell_names |
Calculate ArchR-compatible per-cell QC statistics | qc_scATAC |
Find signed distance to nearest genomic ranges | range_distance_to_nearest |
Read a bed file into a data frame | read_bed read_encode_blacklist |
Read GTF gene annotations | read_gencode_genes read_gencode_transcripts read_gtf |
Read UCSC chromosome sizes | read_ucsc_chrom_sizes |
Rotate ggplot x axis labels | rotate_x_labels |
SCTransform Pearson Residuals | sctransform_pearson |
Subset, translate, or reorder cell IDs | select_cells |
Subset, translate, or reorder chromosome IDs | select_chromosomes |
Subset fragments by genomic region | select_regions |
Adjust trackplot properties | get_trackplot_height set_trackplot_height set_trackplot_label |
Shift start or end coordinates | shift_fragments |
Subset fragments by length | subset_lengths |
Calculate svds | svds |
Calculate ranges x cells tile overlap matrix | tile_matrix |
Combine track plots | trackplot_combine |
Pseudobulk coverage trackplot | trackplot_coverage |
Plot transcript models | trackplot_gene |
Plot loops | trackplot_loop |
Plot scale bar | trackplot_scalebar |
Transpose the storage order for a matrix | transpose_storage_order |
Read/write BPCells fragment objects | open_fragments_dir open_fragments_hdf5 write_fragments_dir write_fragments_hdf5 write_fragments_memory |
Read/write sparse matrices | open_matrix_dir open_matrix_hdf5 write_matrix_dir write_matrix_hdf5 write_matrix_memory |