{"id":38525476,"url":"https://github.com/dputhier/scigenex","last_synced_at":"2026-01-17T06:46:28.095Z","repository":{"id":37727900,"uuid":"307423858","full_name":"dputhier/scigenex","owner":"dputhier","description":"This repository stores the scigenex R library.","archived":false,"fork":false,"pushed_at":"2025-10-15T10:49:03.000Z","size":90940,"stargazers_count":5,"open_issues_count":17,"forks_count":2,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-10-16T03:42:23.225Z","etag":null,"topics":["classification","filtering-algorithm","r","r-package","scrna-seq","scrna-seq-analysis","scrnaseq","unsupervised-learning"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dputhier.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-10-26T15:48:46.000Z","updated_at":"2025-10-15T10:49:08.000Z","dependencies_parsed_at":"2023-09-23T14:23:39.758Z","dependency_job_id":"fbf672e0-dfa0-4e01-b9d5-0699f1b72e54","html_url":"https://github.com/dputhier/scigenex","commit_stats":null,"previous_names":[],"tags_count":52,"template":false,"template_full_name":null,"purl":"pkg:github/dputhier/scigenex","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dputhier%2Fscigenex","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dputhier%2Fscigenex/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dputhier%2Fscigenex/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dputhier%2Fscigenex/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dputhier","download_url":"https://codeload.github.com/dputhier/scigenex/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dputhier%2Fscigenex/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28502877,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T04:31:57.058Z","status":"ssl_error","status_checked_at":"2026-01-17T04:31:45.816Z","response_time":85,"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":["classification","filtering-algorithm","r","r-package","scrna-seq","scrna-seq-analysis","scrnaseq","unsupervised-learning"],"created_at":"2026-01-17T06:46:27.994Z","updated_at":"2026-01-17T06:46:28.089Z","avatar_url":"https://github.com/dputhier.png","language":"R","readme":"---\noutput:\n  md_document:\n    variant: gfm\nhtml_preview: false\n---\n\n\u003c!-- README.md is generated from README.Rmd using devtools::build_readme(). Please edit that file --\u003e\n\n```{r echo=FALSE, results=\"hide\", message=FALSE}\nlibrary(\"badger\")\n```\n\n\u003c!-- \u003cimg src=\"https://raw.githubusercontent.com/dputhier/scigenex/main/inst/sticker/scigenex_logo.png\" width=\"150\"  align=\"right\"/\u003e --\u003e\n\n\n```{r, echo = FALSE, results='asis'}\ncat(\n\tbadge_lifecycle(stage = \"stable\", color=\"green\"),\n\tbadge_repostatus(\"Active\"),\n\tbadge_license(\"MIT\"),\n\tbadge_last_commit(ref=\"dputhier/scigenex\"),\n\tbadge_codecov(\"dputhier/scigenex\")\n)\n```\n\n# SciGeneX repository\n\n## :arrow_double_down: Installation\n\n### System requirements\n\nThe partitioning steps are currently performed using a system call to the Markov Cluster (MCL) algorithm that presently limits the use of DBF-MCL to unix-like platforms. Importantly, the `mcl` command should be in your PATH and reachable from within R (see dedicated section).\n\n### Step 1 - Installation of SciGeneX\n\n#### From R\n\nThe scigenex library is currently not available in CRAN or Bioc. To install from github, use:\n\n\n    devtools::install_github(\"dputhier/scigenex\")\n    library(scigenex)\n\n\n#### From the terminal\n\n\nDownload the *tar.gz* from github or clone the main branch. Uncompress and run the following command from within the uncompressed scigenex folder:\n\n\n    R CMD INSTALL .\n\n\nThen load the library from within R.\n\n\n    library(scigenex)\n\n\n### Step 2 - Installation of MCL\n\nYou may skip this step as the latest versions of SciGeneX will call `scigenex::install_mcl()`to install MCL in `~/.scigenex` directory if this program is not found in the PATH.\n\n#### Installation of MCL using install_mcl()\n\nThe `install_mcl()` has been developed to ease MCL installation. This function should be call automatically from within R when calling the `gene_clustering()` function. If `install_mcl()` does not detect MCL in the PATH it will install it in `~/.scigenex`.\n\n\n#### Installation of MCL from source\n\nOne also can install MCL from source using the following code.\n\n    # Download the latest version of mcl \n    wget http://micans.org/mcl/src/mcl-latest.tar.gz\n    # Uncompress and install mcl\n    tar xvfz mcl-latest.tar.gz\n    cd mcl-xx-xxx\n    ./configure\n    make\n    sudo make install\n    # You should get mcl in your path\n    mcl -h\n\n\n#### Installation of MCL from sources\n\nFinally you may install MCL using conda. Importantly, the mcl command should be available in your PATH from within R.\n\n    conda install -c bioconda mcl\n\n## Example\n\nThe scigenex library contains several datasets including the pbmc3k_medium which is a subset from pbmc3k 10X dataset.\n\n\n  \tlibrary(Seurat)\n  \tlibrary(scigenex)\n  \tset_verbosity(1)\n  \n  \t# Load a dataset\n  \tload_example_dataset(\"7871581/files/pbmc3k_medium\")\n  \n  \t# Select informative genes\n  \tres \u003c- select_genes(pbmc3k_medium,\n  \t                     distance = \"pearson\",\n  \t                     row_sum=5)\n  \t                     \n  \t# Cluster informative features\n  \t \n  \t## Construct and partition the graph\n  \tres \u003c- gene_clustering(res, \n  \t                       inflation = 1.5, \n  \t                       threads = 4)\n  \t                        \n  \t# Display the heatmap of gene clusters\n  \tres \u003c- top_genes(res)\n  \tplot_heatmap(res, cell_clusters = Seurat::Idents(pbmc3k_medium))\n\n## :book: Documentation\n\nDocumentation (in progress) is available at [https://dputhier.github.io/scigenex/](https://dputhier.github.io/scigenex/).\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdputhier%2Fscigenex","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdputhier%2Fscigenex","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdputhier%2Fscigenex/lists"}