Matrix Market Utility for R

This R package contains a list of functions that can be useful in processing single-cell RNA-seq data generated by 10x Genomics with simplicity and memory-efficiency.

Design philosophy (that you may not like)

• Do not attempt to populate everything in memory

• Avoid using R class objects (or a list of lists)

• Column (cell) indexing to achieve scalable random access

• Hopefully, one function does one thing

Installation

$ R CMD INSTALL mmutilR_${version}.tar.gz

or

> devtools::install_github("causalpathlab/mmutilR@main")

Available functions

Data editing

• mmutilR::rcpp_mmutil_copy_selected_columns

• mmutilR::rcpp_mmutil_copy_selected_rows

• mmutilR::rcpp_mmutil_merge_file_sets

Data analysis

• mmutilR::rcpp_mmutil_compute_scores

• mmutilR::rcpp_mmutil_aggregate

• mmutilR::rcpp_mmutil_bbknn_pca

• mmutilR::rcpp_mmutil_pca

Random access

• mmutilR::rcpp_mmutil_read_index

• mmutilR::rcpp_mmutil_build_index

• mmutilR::rcpp_mmutil_check_index

• mmutilR::rcpp_mmutil_read_columns

Marker-based cell type annotation

• mmutilR::rcpp_mmutil_annotate_columns

• mmutilR::run.annotation

Matching between columns

• mmutilR::rcpp_mmutil_match_files

Simulation

• mmutilR::simulate_gamma_glm

• mmutilR::rcpp_mmutil_simulate_poisson

Contact

Yongjin Park ypp@stat.ubc.ca