{"id":32206281,"url":"https://github.com/liuy12/scdeconr","last_synced_at":"2025-10-22T05:14:04.942Z","repository":{"id":175063199,"uuid":"624690351","full_name":"Liuy12/SCdeconR","owner":"Liuy12","description":"Deconvolution of bulk RNA-seq data using single-cell RNA-seq data as reference","archived":false,"fork":false,"pushed_at":"2025-07-14T16:11:36.000Z","size":40708,"stargazers_count":6,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-09-24T10:57:37.905Z","etag":null,"topics":["bulk-rna-seq-deconvolution","deconvolution","differential-expression","ffpe","geneset-enrichment-analysis","r","scdeconr","single-cell"],"latest_commit_sha":null,"homepage":"https://liuy12.github.io/SCdeconR/","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Liuy12.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE.md","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}},"created_at":"2023-04-07T03:07:29.000Z","updated_at":"2025-09-18T13:19:54.000Z","dependencies_parsed_at":null,"dependency_job_id":"8a7bb92a-7e0c-4a9e-ba15-a7facd8c98e9","html_url":"https://github.com/Liuy12/SCdeconR","commit_stats":null,"previous_names":["liuy12/scdeconr"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Liuy12/SCdeconR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Liuy12%2FSCdeconR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Liuy12%2FSCdeconR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Liuy12%2FSCdeconR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Liuy12%2FSCdeconR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Liuy12","download_url":"https://codeload.github.com/Liuy12/SCdeconR/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Liuy12%2FSCdeconR/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280383000,"owners_count":26321423,"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","status":"online","status_checked_at":"2025-10-22T02:00:06.515Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["bulk-rna-seq-deconvolution","deconvolution","differential-expression","ffpe","geneset-enrichment-analysis","r","scdeconr","single-cell"],"created_at":"2025-10-22T05:14:01.994Z","updated_at":"2025-10-22T05:14:04.936Z","avatar_url":"https://github.com/Liuy12.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SCdeconR\n\n\u003cimg src=\"man/figures/SCdeconR.png\" alt=\"\" align=\"middle\" width=\"100%\" height=\"100%\"\u003e\n\nSCdeconR aims to provide a streamlined workflow from deconvolution of bulk RNA-seq data to downstream differential and gene-set enrichment analysis. SCdeconR provides a simulation framework to generate artificial bulk samples for benchmarking purposes. It also provides various visualization options to compare the influence of adjusting for cell-proportions differences on differential expression and pathway analyses. \n\n## Installation\n\n``` r\n# install devtools if it's not installed already\nif (!require(\"devtools\", quietly = TRUE)) install.packages(\"devtools\")\ndevtools::install_github(\"liuy12/SCdeconR\")\n```\n\nTo use [scaden](https://github.com/KevinMenden/scaden) within SCdeconR, follow the below steps:\n\n```r\n# install reticulate package first\ninstall.packages(\"reticulate\")\n```\n\nIntall scaden python package:\n\nUse pip: \n\n`pip install scaden`\n\nOr use Conda:\n\n`conda install scaden`\n\nThen provide your desired python path (that have scaden installed) to option `pythonpath` for function `scdecon`. You should be good to go. \n\nThe following packages are optional, and only needed for specific methods within SCdeconR. \n\n``` r\n# install BiocManager if it's not installed already\nif (!require(\"BiocManager\", quietly = TRUE)) install.packages(\"BiocManager\")\n\n# data normalization\n## scater\nBiocManager::install(\"scater\")\n\n## scran\nBiocManager::install(\"scran\")\n\n## Linnorm\nBiocManager::install(\"Linnorm\")\n\n## SingleCellExperiment\nBiocManager::install(\"SingleCellExperiment\")\n\n# deconvolution methods\n## FARDEEP\ninstall.packages(\"FARDEEP\")\n\n## nnls\ninstall.packages(\"nnls\")\n\n## MuSiC\ndevtools::install_github('xuranw/MuSiC')\n\n## SCDC\ndevtools::install_github(\"meichendong/SCDC\")\n\n# differential expression\n## DESeq2\nBiocManager::install(\"DESeq2\")\n\n# cell-type specific gene expression\n## spacexr\ndevtools::install_github(\"dmcable/spacexr\", build_vignettes = FALSE)\n\n# interactive plot\ninstall.packages(\"plotly\")\n```\n\n## Usage\n\n```r\nlibrary(SCdeconR)\n```\n\nSee [here](https://liuy12.github.io/SCdeconR/) for detailed documentation and tutorials. \n\nSee [here](https://htmlpreview.github.io/?https://github.com/Liuy12/SCdeconR/blob/master/inst/reprod_doc/Reproducible_document.html) for a document to reproduce the results from the study.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fliuy12%2Fscdeconr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fliuy12%2Fscdeconr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fliuy12%2Fscdeconr/lists"}