{"id":13592288,"url":"https://github.com/marchinilab/dropsim","last_synced_at":"2025-04-08T23:31:49.792Z","repository":{"id":201785167,"uuid":"88439108","full_name":"marchinilab/dropsim","owner":"marchinilab","description":"R Package for Single Cell RNAseq Synthetic Data Simulation","archived":false,"fork":false,"pushed_at":"2018-03-14T11:19:19.000Z","size":1320,"stargazers_count":5,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-08-02T16:44:31.270Z","etag":null,"topics":["r-package","scrnaseq","simulation","single-cell"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/marchinilab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-04-16T19:55:28.000Z","updated_at":"2022-09-13T15:14:06.000Z","dependencies_parsed_at":null,"dependency_job_id":"f3e4bd31-122b-44df-b778-f1803d07205f","html_url":"https://github.com/marchinilab/dropsim","commit_stats":null,"previous_names":["marchinilab/dropsim"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marchinilab%2Fdropsim","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marchinilab%2Fdropsim/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marchinilab%2Fdropsim/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marchinilab%2Fdropsim/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/marchinilab","download_url":"https://codeload.github.com/marchinilab/dropsim/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223346616,"owners_count":17130470,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["r-package","scrnaseq","simulation","single-cell"],"created_at":"2024-08-01T16:01:07.706Z","updated_at":"2024-11-06T13:30:50.085Z","avatar_url":"https://github.com/marchinilab.png","language":"R","funding_links":[],"categories":["Software packages"],"sub_categories":["RNA-seq","Simulation"],"readme":"# dropsim: Single Cell RNAseq Simulator\n\nThis is an R package for quickly simulating single cell RNAseq read count data. The model is based on data from droplet based methods, for other methods [Splatter](https://github.com/Oshlack/splatter) may be better suited. Sinsynthr shares a similar core model to Splatter but is overall much simpler.\n\n## Installation\n\n```R\n# install.packages(\"devtools\")\ndevtools::install_github(\"marchinilab/dropsim\")\n```\n\n## Quick Start\n```R\nlibrary(dropsim)\n\n# Use default parameters\nnew_parameters \u003c- dropsim_parameters()\n\n# Simulate counts\nsimulation \u003c- simulateDGE(new_parameters)\n\n# Normalise Counts matrix\nnormalised_dge \u003c- normaliseDGE(simulation$counts)\n\n# Do a PCA to check\ndge_pca \u003c- prcomp(normalised_dge)\nqplot(dge_pca$x[,1], dge_pca$x[,2], colour=rownames(dge_pca$x)) + labs(colour=\"Group\", y=\"PC2\", x=\"PC1\")\n```\n\n![PCA on simulated data](example.png)\n\nFor more detailed examples of how to use this package please see the [vignette](vignettes/vignette.md).\n\n## Directory Organisation\nThe [R/](R/) directory contains source code of the functions to simulate the data.\n\nThe [man/](man/) directory contains the manual pages for the functions, compiled by roxygen.\n\nThe [vignettes/](vignettes/) directory contains uncompiled Rmarkdown with examples of use.\n\nThe [tests/](tests/) directory contains the unit tests which are carried out by the testthat R package.\n\nContributions of any size or form are welcome!","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarchinilab%2Fdropsim","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmarchinilab%2Fdropsim","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarchinilab%2Fdropsim/lists"}