{"id":19629353,"url":"https://github.com/drisso/zinbwave","last_synced_at":"2025-09-07T11:31:09.355Z","repository":{"id":87897872,"uuid":"101932832","full_name":"drisso/zinbwave","owner":"drisso","description":"Clone of the Bioconductor repository for the zinbwave package, see https://bioconductor.org/packages/zinbwave","archived":false,"fork":false,"pushed_at":"2024-03-13T20:20:22.000Z","size":665,"stargazers_count":43,"open_issues_count":10,"forks_count":10,"subscribers_count":7,"default_branch":"master","last_synced_at":"2024-12-17T13:51:37.855Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","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/drisso.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":"2017-08-30T22:00:06.000Z","updated_at":"2024-08-24T17:41:18.000Z","dependencies_parsed_at":"2024-11-11T11:58:46.319Z","dependency_job_id":"feb589a0-9c15-4bcd-876d-62336650efd0","html_url":"https://github.com/drisso/zinbwave","commit_stats":{"total_commits":142,"total_committers":12,"mean_commits":"11.833333333333334","dds":0.5915492957746479,"last_synced_commit":"712b11d095567477d130478e3be6eaa966d2f129"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drisso%2Fzinbwave","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drisso%2Fzinbwave/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drisso%2Fzinbwave/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/drisso%2Fzinbwave/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/drisso","download_url":"https://codeload.github.com/drisso/zinbwave/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":231949229,"owners_count":18450463,"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":[],"created_at":"2024-11-11T11:58:38.442Z","updated_at":"2025-01-02T14:10:58.492Z","avatar_url":"https://github.com/drisso.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# zinbwave\nZero-inflated Negative Binomial based Wanted Variation Extraction (ZINB-WaVE)\n\n[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)\n[![BioC release](http://www.bioconductor.org/shields/build/release/bioc/zinbwave.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/zinbwave)\n[![BioC devel](http://www.bioconductor.org/shields/build/release/bioc/zinbwave.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/zinbwave)\n[![R-CMD-check](https://github.com/drisso/zinbwave/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/drisso/zinbwave/actions)\n[![Coverage](https://codecov.io/gh/drisso/zinbwave/branch/master/graph/badge.svg)](https://codecov.io/gh/drisso/zinbwave)\n\nThis package implements a zero-inflated negative binomial model for single-cell RNA-seq data, with latent factors.\n\nThe model is described in details in the paper:\n\n[D. Risso, F. Perraudeau, S. Gribkova, S. Dudoit and JP. Vert (2018).\nA general and flexible method for signal extraction from single-cell RNA-seq data. Nature Communications.](https://www.nature.com/articles/s41467-017-02554-5)\n\n## Installation\n\nSince Bioconductor 3.7 the new recommended way to install Bioconductor packages is via the BiocManager package, available on CRAN:\n\n```{r}\ninstall.packages(\"BiocManager\")\nBiocManager::install(\"zinbwave\")\n```\n\nNote that `zinbwave` requires `R (\u003e=3.4)` and `Bioconductor (\u003e=3.6)`.\n\nIn virtually all cases, installing from Bioconductor is recommended. However, if you want to install the development version of `zinbwave` from GitHub, you can do so with the following.\n\n```{r}\nlibrary(devtools)\ninstall_github(\"drisso/zinbwave\")\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdrisso%2Fzinbwave","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdrisso%2Fzinbwave","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdrisso%2Fzinbwave/lists"}