{"id":18046643,"url":"https://github.com/ltla/matrixeval2017","last_synced_at":"2026-01-18T17:06:33.475Z","repository":{"id":82716812,"uuid":"92600755","full_name":"LTLA/MatrixEval2017","owner":"LTLA","description":"Evaluating access and memory usage of different matrix types","archived":false,"fork":false,"pushed_at":"2018-08-08T11:38:13.000Z","size":373,"stargazers_count":4,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-05T04:26:00.804Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LTLA.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-05-27T13:36:10.000Z","updated_at":"2019-04-04T14:33:28.000Z","dependencies_parsed_at":null,"dependency_job_id":"16f6d6f7-dc8b-4234-877d-ad2debc0b241","html_url":"https://github.com/LTLA/MatrixEval2017","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/LTLA/MatrixEval2017","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FMatrixEval2017","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FMatrixEval2017/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FMatrixEval2017/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FMatrixEval2017/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LTLA","download_url":"https://codeload.github.com/LTLA/MatrixEval2017/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FMatrixEval2017/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28543743,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-18T14:59:57.589Z","status":"ssl_error","status_checked_at":"2026-01-18T14:59:46.540Z","response_time":98,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-30T19:08:22.048Z","updated_at":"2026-01-18T17:06:33.458Z","avatar_url":"https://github.com/LTLA.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Evaluating the performance of different matrix types\n\n## Overview \n\nThis repository contains code for the paper **beachmat: a Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types** \nby [Lun _et al._ (2018)](https://doi.org/10.1371/journal.pcbi.1006135).\n\nThe provided code will check the performance of different matrix types for row/column access, using simulated and real data sets.\nTo run the tests on your machine, please read the following instructions.\n\n## Setup\n\n1. Install [_beachmat_](https://bioconductor.org/packages/beachmat) from Bioconductor.\n2. Enter `timings` and run `R CMD INSTALL --clean package`.\nThis requires installation of _RcppArmadillo_ and _RcppEigen_. \n\n## Running simulations\n  \n- `timings/` contains scripts for timings (in milliseconds) for accessing data from different matrix representations.\n- `timings/chunking/` contains scripts for timing rechunking, as well as checking the chunk cache logic.\n- `memory/` contains scripts for memory usage for different matrix representations.\n- `miscellaneous` contains scripts to compare timings to R, and to verify the no-copy access method of _RcppArmadillo_ and _RcppEigen_.\n\n## Running real analyses\n\n### Zeisel dataset\n\nEnter `real/zeisel` and download the [count matrix for the Zeisel data set](https://storage.googleapis.com/linnarsson-lab-www-blobs/blobs/cortex/expression_mRNA_17-Aug-2014.txt).\n\n- Execute the `zeisel_time.R` script to generate timings (in milliseconds) for matrix access to this data.\nThis will also determine memory usage for each matrix representation.\n- Execute the `detection_stats.R` script to generate timings (in milliseconds) for computing various cell- or gene-based statistics from this data.\n\n### 10X dataset\n\nEnter `real/10X` and install [_TENxBrainData_](https://bioconductor.org/packages/TENxBrainData).\nRead the `README.md` file for order of evaluation of the various Rmarkdown scripts.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fmatrixeval2017","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fltla%2Fmatrixeval2017","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fmatrixeval2017/lists"}