Skip to content

v0.1.0
Compare
Choose a tag to compare
@bnprks bnprks released this 10 Apr 00:10
· 152 commits to main since this release
v0.1.0
5af6cd8
This commit was signed with the committer’s verified signature.
bnprks Ben Parks
GPG key ID: 0BF0A1EFA66292E2
Learn about vigilant mode.

This is the first tagged release of BPCells, though breaking API changes are still possible prior to 1.0

Features

  • ATAC-seq Analysis
    • Reading/writing 10x fragment files on disk
    • Reading/writing compressed fragments on disk (in folder or hdf5 group)
    • Interconversion of fragments objects with GRanges / data.frame
    • Merging of multiple source fragment files transparently at run time
    • Calculation of Cell x Peak matrices, and Cell x Tile matrices
    • ArchR-compatible QC calculations
    • ArchR-compatible gene activity score calculations
    • Filtering fragments by chromosmes, cells, lengths, or genomic region
    • Fast peak calling approximation via overlapping tiles
  • Single cell matrices
    • Conversion to/from R sparse matrices
    • Read-write access to 10x hdf5 feature matrices, and read-only access to AnnData files
    • Reading/writing of compressed matrices on disk (in folder or hdf5 group)
    • Support for integer or single/double-precision floating point matrices on disk
    • Fast transposition of storage order, to switch between indexing by cell or
      by gene/feature.
    • Concatenation of multiple source matrix files transparently at run time
    • Single-pass calculation of row/column mean and variance
    • Wilcoxon marker feature calculation
    • Transparent handling of vector +, -, *, /, and log1p for streaming
      normalization, along with other less common operations. This allows implementation of ATAC-seq LSI and Seurat default
      normalization, along with most published log-based normalizations.
    • SCTransform pearson residual calculation
    • Multiplication of sparse matrices
  • Single cell plotting utilities
    • Read count knee cutoffs
    • UMAP embeddings
    • Dot plots
    • Transcription factor footprinting / TSS profile plotting
    • Fragments vs. TSS Enrichment ATAC-seq QC plot
    • Pseudobulk genome track plots, with gene annotation plots
  • Additional utility functions
    • Matching gene symbols/IDs to canonical symbols
    • Download transcript annotations from Gencode or GTF files
    • Download + parse UCSC chromosome sizes
    • Parse peak files BED format; Download ENCODE blacklist region
    • Wrappers for knn graph calculation + clustering

Note: All operations interoperate with all storage formats. For example, all matrix operations can be applied directly to an AnnData or 10x matrix file. In many cases
the bitpacking-compressed formats will provide performance/space advantages, but
are not required to use the computations.

Assets 2
Loading