/mmutilR

Primary LanguageC++MIT LicenseMIT

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