R package to process BUS files
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BUSpaRse

This package processes bus files generated from raw single-cell RNA-seq data, e.g. using kallisto. The bus format is a table with 4 columns: Barbode, UMI, Set, and counts, that represent scRNA-seq datasets. The main goal of this package is to parse bus format in R into a sparse matrix that can be used for downstream analysis, such as with Seurat and SingleCellExperiment. See this paper for more information about the bus format.

Installation

You can install BUSpaRse with:

if (!require(devtools)) install.packages("devtools")
devtools::install_github("BUStools/BUSpaRse")

This is work in progress. The package will be available on Bioconductor shortly.

Installation note: This package contains compiled code. MacOS users using R 3.5 should download and install Clang 6.0 and gfortran 6.1 compilers from this webpage. R 3.5 no longer works with Clang 4, which was used for R 3.4.

Example

See the vignettes for examples of using BUSpaRse. The vignettes contain a complete walk-through, starting with downloading of the FASTQ files for an experiment and ending with an analysis. There are currently vignettes for 10x v2 and 10x v3 technology datasets (Drop-seq, inDrops, and CEL-seq2 coming soon).