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
SingleCellExperiment. See this paper for more information about the
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.
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).