{"id":18046655,"url":"https://github.com/ltla/pcselection2018","last_synced_at":"2026-01-19T11:02:06.818Z","repository":{"id":82716827,"uuid":"141807683","full_name":"LTLA/PCSelection2018","owner":"LTLA","description":"Some comments on how to determine the number of PCs to retain.","archived":false,"fork":false,"pushed_at":"2018-09-18T12:02:39.000Z","size":143,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-05T04:26:01.145Z","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}},"created_at":"2018-07-21T11:53:58.000Z","updated_at":"2021-03-10T16:37:54.000Z","dependencies_parsed_at":null,"dependency_job_id":"140fe8ea-ca28-458b-a374-ca206d944176","html_url":"https://github.com/LTLA/PCSelection2018","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/LTLA/PCSelection2018","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FPCSelection2018","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FPCSelection2018/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FPCSelection2018/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FPCSelection2018/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LTLA","download_url":"https://codeload.github.com/LTLA/PCSelection2018/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FPCSelection2018/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28565876,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-19T08:53:44.001Z","status":"ssl_error","status_checked_at":"2026-01-19T08:52:40.245Z","response_time":67,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":"2024-10-30T19:08:24.010Z","updated_at":"2026-01-19T11:02:06.798Z","avatar_url":"https://github.com/LTLA.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Discussion of PC selection methods for scRNA-seq data\n\nThis repository contains some scripts to assess different methods of choosing the number of PCs to retain.\nThe `text` directory contains LaTeX files for the report, a compiled PDF of which can be found [here](https://jmlab-gitlab.cruk.cam.ac.uk/miscellaneous/technical-reports/raw/master/pc-selection.pdf).\nThe `simulations` directory contains R scripts for performing the basic simulations:\n\n- `functions.R`, a central R script containing definitions of useful functions for the simulations.\n- `sim_gaussclust.R`, a template for simulations of clusters with Gaussian noise.\n- `sim_trajectory.R`, a tempalte for simulations of trajectories between multiple nodes.\n- `submitter.sh`, a Bash script for SLURM job submission of the simulations.\n- `plot_results.R`, an R script to generate the plots.\n- `simulate_noise.R`, an R script examining the effect of removing biological noise.\n\nThe `real` directory contains R scripts for performing the real data-based simulations:\n\n- `proc_kolod.R`, an R script for pre-processing the mESC data set.\n- `proc_pbmc4k.R`, an R script for pre-processing the PBMC data set.\n- `run_kolod.R`, a template for performing simulations based on the mESC data set.\n- `run_pbmc4k.R`, a template for performing simulations based on the PBMC data set.\n- `submitter.sh`, a Bash script for SLURM job submission of the simulations.\n- `plot_results.R`, an R script to generate the plots.\n\nIn addition, `batching/batching.Rmd` contains an example of how batch removal in the presence of zeroes can distort the PCA results.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fpcselection2018","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fltla%2Fpcselection2018","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fpcselection2018/lists"}