{"id":28381096,"url":"https://github.com/idsia/clier","last_synced_at":"2025-06-25T01:32:05.126Z","repository":{"id":275733992,"uuid":"897985766","full_name":"IDSIA/CLIER","owner":"IDSIA","description":"Repository for the article \"Protocol for interpretable and context-specific single-cell informed deconvolution of bulk RNA-seq data\" (STAR Protocols, 2025)","archived":false,"fork":false,"pushed_at":"2025-03-14T13:43:30.000Z","size":12142,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-05-30T03:40:14.642Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","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/IDSIA.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":"2024-12-03T15:31:21.000Z","updated_at":"2025-03-14T13:43:33.000Z","dependencies_parsed_at":"2025-03-06T12:33:20.070Z","dependency_job_id":null,"html_url":"https://github.com/IDSIA/CLIER","commit_stats":null,"previous_names":["idsia/clier"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/IDSIA/CLIER","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IDSIA%2FCLIER","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IDSIA%2FCLIER/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IDSIA%2FCLIER/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IDSIA%2FCLIER/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/IDSIA","download_url":"https://codeload.github.com/IDSIA/CLIER/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IDSIA%2FCLIER/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261785260,"owners_count":23209274,"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":"2025-05-30T03:38:03.309Z","updated_at":"2025-06-25T01:32:05.016Z","avatar_url":"https://github.com/IDSIA.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CLIER\n\nThis repository contains code and test data for the article [**\"Protocol for interpretable and context-specific single-cell informed deconvolution of bulk RNA-seq data,\"**](https://www.sciencedirect.com/science/article/pii/S2666166725000760?via%3Dihub) published in STAR Protocols (Malpetti, Mangili et al., 2025).\n\n## Detailed Description of Files\n\n### Code\n- **protocol_code.R**: Contains the lines of code included in the manuscript (excluding the processing from FASTQ to TPM).\n- **aux_functions.R**: Contains all the R functions necessary for executing the protocol.\n- **align_fastq.sh**: Automates the process of downloading FASTQ files and aligning paired-end RNA-Seq data using the STAR aligner.\n\n### Data\n- **kidney_atlas_matrix.rds**: Contains the single-cell signatures atlas built in [**\"A transfer learning framework to elucidate the clinical relevance of altered proximal tubule cell states in kidney disease,\"**](https://www.sciencedirect.com/science/article/pii/S2589004224004929) published in iScience (Legouis, Rinaldi, Malpetti et al., 2024).\n- **kidney_atlas_info.xlsx**: Contains descriptions of the signatures included in the single-cell signatures atlas built in the above study.\n- **DKD_tpm.rds**: Contains a processed version (TPM) of the dataset GSE142025, also used in the above study.\n- **DKD_clin.rds**: Contains clinical information (fibrosis) regarding the dataset GSE142025.\n- **genelength.txt**: Contains genes length (to be used in data processing).\n\n## On the Execution\n\nThe code in **protocol_code.R** can be fully executed using the test data provided in this repository. Users who might want to skip the training phase (that takes approximately 9 hours) and test a pre-trained model can find the KCLIER model [here](https://drive.switch.ch/index.php/s/OpvMh1vGRgRmKKf), together with other intermediate files produced during the execution. We share these file separately since, given their large size, they cannot fit on GitHub.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fidsia%2Fclier","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fidsia%2Fclier","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fidsia%2Fclier/lists"}