Package: BPCells 0.2.0
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:
BPCells_0.2.0.tar.gz
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BPCells.pdf |BPCells.html✨
BPCells/json (API)
NEWS
| # Install 'BPCells' in R: |
| install.packages('BPCells', repos = c('https://bnprks.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 1 days agofrom:1e1678f34b. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 16 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 16 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 16 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 16 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 16 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 16 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 16 2024 |
| R-4.3-mac-x86_64 | WARNING | Nov 16 2024 |
| R-4.3-mac-aarch64 | WARNING | Nov 16 2024 |
Exports:add_colsadd_rowsall_matrix_inputsall_matrix_inputs<-apply_by_colapply_by_rowas.data.frameas.matrixbinarizecall_macs_peakscall_peaks_macscall_peaks_tilecanonical_gene_symbolcellNamescellNames<-checksumchrNameschrNames<-cluster_graph_leidencluster_graph_louvaincluster_graph_seuratcollect_featurescolMaxscolMaxs.defaultcolMaxs.IterableMatrixcolMeanscolQuantilescolQuantiles.defaultcolQuantiles.IterableMatrixcolSumscolVarscolVars.defaultcolVars.IterableMatrixcontinuous_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_scatterprefix_cell_namespseudobulk_matrixqc_scATACrange_distance_to_nearestread_bedread_encode_blacklistread_gencode_genesread_gencode_transcriptsread_gtfread_ucsc_chrom_sizesregress_outrotate_x_labelsrowMaxsrowMaxs.defaultrowMaxs.IterableMatrixrowMeansrowQuantilesrowQuantiles.defaultrowQuantiles.IterableMatrixrowSumsrowVarsrowVars.defaultrowVars.IterableMatrixsctransform_pearsonselect_cellsselect_chromosomesselect_regionsset_trackplot_heightset_trackplot_labelshift_fragmentsstorage_ordersubset_lengthssvdsttile_matrixtrackplot_bulktrackplot_combinetrackplot_coveragetrackplot_genetrackplot_genome_annotationtrackplot_looptrackplot_scalebartranspose_storage_orderwrite_fragments_10xwrite_fragments_dirwrite_fragments_hdf5write_fragments_memorywrite_insertion_bedgraphwrite_matrix_10x_hdf5write_matrix_anndata_hdf5write_matrix_dirwrite_matrix_hdf5write_matrix_memory
Dependencies:bitbit64clicliprcolorspacecpp11crayondplyrfansifarvergenericsggplot2ggrepelgluegtablehexbinhmsisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepatchworkpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppEigenreadrrlangscalesscattermorestringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr
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<- |
| Apply a function to summarize rows/cols | apply_by_col apply_by_row |
| Convert matrix elements to zeros and ones | binarize |
| Call peaks using MACS2/3 | call_peaks_macs |
| 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 colMaxs colMeans,IterableMatrix-method colQuantiles colSums,IterableMatrix-method colVars expm1,IterableMatrix-method expm1_slow IterableMatrix-methods log1p,IterableMatrix-method log1p_slow matrix_type round,IterableMatrix-method rowMaxs rowMeans,IterableMatrix-method rowQuantiles rowSums,IterableMatrix-method rowVars 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 |
| Aggregate counts matrices by cell group or feature. | pseudobulk_matrix |
| 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 |
| Regress out unwanted variation | regress_out |
| 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 range-based annotation tracks (e.g. peaks) | trackplot_genome_annotation |
| 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 |
| Write insertion counts to bedgraph file | write_insertion_bedgraph |
| Read/write sparse matrices | open_matrix_dir open_matrix_hdf5 write_matrix_dir write_matrix_hdf5 write_matrix_memory |