{"id":27885908,"url":"https://github.com/kris96tian/scrna-webapp","last_synced_at":"2026-07-13T15:31:34.730Z","repository":{"id":273691973,"uuid":"920561657","full_name":"kris96tian/scRNA-WebApp","owner":"kris96tian","description":"Interactive web application  for analyzing scRNA-seq data using Scanpy","archived":false,"fork":false,"pushed_at":"2025-01-22T11:38:37.000Z","size":13,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-10-26T01:03:19.413Z","etag":null,"topics":["scanpy","scrna-seq-analysis","single-cell-rna-seq"],"latest_commit_sha":null,"homepage":"https://scrna-webapp.streamlit.app/","language":"Python","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/kris96tian.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":"2025-01-22T11:22:37.000Z","updated_at":"2025-01-22T11:38:40.000Z","dependencies_parsed_at":"2025-01-22T12:29:02.042Z","dependency_job_id":"e20684bc-d2d4-444e-a870-9e78479f6d13","html_url":"https://github.com/kris96tian/scRNA-WebApp","commit_stats":null,"previous_names":["kris96tian/scrna-webapp"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/kris96tian/scRNA-WebApp","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kris96tian%2FscRNA-WebApp","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kris96tian%2FscRNA-WebApp/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kris96tian%2FscRNA-WebApp/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kris96tian%2FscRNA-WebApp/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kris96tian","download_url":"https://codeload.github.com/kris96tian/scRNA-WebApp/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kris96tian%2FscRNA-WebApp/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35427834,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-13T02:00:06.543Z","response_time":119,"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":["scanpy","scrna-seq-analysis","single-cell-rna-seq"],"created_at":"2025-05-05T07:49:37.524Z","updated_at":"2026-07-13T15:31:34.709Z","avatar_url":"https://github.com/kris96tian.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"## scRNA-Scanpy-WebApp  \n\nVisit App:  https://scrna-webapp.streamlit.app/\n\n\u003cimg src=\"blob:chrome-untrusted://media-app/d7244cbd-044a-4cb8-b393-27546b9d6773\"/\u003e![image](https://github.com/user-attachments/assets/4fa04a1b-8be2-4d9d-b394-9565e02cf60d)\n\n\n### Overview  \nThis **Streamlit**-based web application provides an interactive platform for processing and analyzing single-cell RNA sequencing (scRNA-seq) data using **Scanpy**. Workflow includes data upload, quality control (QC), normalization, dimensionality reduction, clustering, and marker discovery.\n\n---\n\n### Features  \n- **Data Upload \u0026 QC**  \n  - Supports multiple formats: `10x Genomics (H5)`, `AnnData (H5AD)`, `CSV`, `MTX`, `Loom`, and Excel.  \n  - Automated detection of mitochondrial, ribosomal, and hemoglobin genes for QC.  \n  - Violin and scatter plots for visualizing quality metrics.\n\n- **Processing**  \n  - Doublet detection with Scrublet.  \n  - Data normalization and log transformation.  \n  - Highly variable gene selection (HVG).\n\n- **Dimensionality Reduction**  \n  - PCA for feature space reduction.  \n  - Interactive sliders for parameter tuning.\n\n- **Clustering \u0026 Visualization**  \n  - UMAP and t-SNE integration.  \n  - Leiden clustering with resolution adjustments.\n\n- **Marker Discovery**  \n  - Differential expression analysis for marker genes.  \n  - Heatmaps and rank plots for visualizing key markers.\n\n---\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkris96tian%2Fscrna-webapp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkris96tian%2Fscrna-webapp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkris96tian%2Fscrna-webapp/lists"}