BUSpaRse

BUSpaRse manipulates barcode, UMI, and set (BUS) format files as data frames in R and converts them into gene count or transcript compatibility counts (TCC) matrices for single cell RNA-seq downstream analysis.

Key Features:

• BUS File Manipulation: Reads and manipulates BUS format files as data frames in R for conversion to gene count or TCC matrices.
• Transcriptome Filtering: Filters biotypes, removes scaffolds and haplotypes, and extracts the filtered transcriptome to disk.
• Transcript-Gene Mapping: Implements utility functions to get transcripts and associated genes required for BUS to gene count matrix conversion, and writes transcript to gene information in bustools format.
• Sparse Matrix Import: Reads bustools output into R as sparse matrices.
• RNA Velocity Support: Generates files required to produce gene count matrices for spliced and unspliced transcripts for RNA velocity analysis.

Scientific Applications:

• Single Cell RNA-seq Quantification: Converts single cell RNA-seq reads from fastq files into gene count or TCC matrices via the kallisto | bustools pipeline.
• RNA Velocity Analysis: Enables generation of spliced and unspliced transcript count matrices to infer cell state dynamics and differentiation trajectories.

Methodology:

BUSpaRse is implemented in R and Rcpp, leveraging data frame manipulation for BUS file processing and sparse matrix representation for efficient storage of count data.