{"id":29303575,"url":"https://github.com/scverse/202504_workshop_gscn","last_synced_at":"2026-03-16T04:33:29.042Z","repository":{"id":284748359,"uuid":"943968505","full_name":"scverse/202504_workshop_GSCN","owner":"scverse","description":null,"archived":false,"fork":false,"pushed_at":"2025-04-17T20:38:49.000Z","size":113019,"stargazers_count":3,"open_issues_count":11,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-18T10:39:27.840Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/scverse.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,"zenodo":null}},"created_at":"2025-03-06T15:08:17.000Z","updated_at":"2025-04-17T20:38:53.000Z","dependencies_parsed_at":null,"dependency_job_id":"8851905c-7af9-4e0c-b221-755ff203a53f","html_url":"https://github.com/scverse/202504_workshop_GSCN","commit_stats":null,"previous_names":["scverse/202504_workshop_gscn"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/scverse/202504_workshop_GSCN","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2F202504_workshop_GSCN","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2F202504_workshop_GSCN/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2F202504_workshop_GSCN/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2F202504_workshop_GSCN/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/202504_workshop_GSCN/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2F202504_workshop_GSCN/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263996091,"owners_count":23541402,"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":"2025-07-07T01:09:13.515Z","updated_at":"2026-03-16T04:33:29.005Z","avatar_url":"https://github.com/scverse.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Overview\n\n## Before the event\n\n### Tech setup\nIn addition to the actual workshop, we offer two pre-workshop sessions designed to help participants with any issues installing software required for the workshop. During these, we also encourage participants to ask questions about basic Python/Jupyter Notebook usages (the notebook discussed in these sessions can be found [here](https://github.com/scverse/202504_workshop_GSCN/blob/main/misc/pre-workshop/pre_workshop_session.ipynb)). The two sessions take place on:\n\n- Wednesday (02.04.2025), 15:00 - 17:00 CET \n- Thursday (03.04.2025), 15:30 - 17:30 CET \n\nThe Zoom links to these events can be found in the mail sent on Sunday, 30.03.2025. If you have any other questions, please direct them to the [2025-04: Workshop GSCN \u003e pre-workshop support](https://scverse.zulipchat.com/#narrow/channel/493335-2025-04.3A-Workshop-GSCN/topic/pre-workshop.20support/with/509718455) Zulip channel.\n\n\n## Syllabus\n\n*Note: Schedule subject to minor adjustments.*\n\n| Date                         | Time          | Activity                                  |\n|------------------------------|---------------|-------------------------------------------|\n| **Monday, 07.04.2025**       | 09:00 – 09:15 | Welcome \u0026 Introduction to the Workshop    |\n|                              | 09:15 – 10:00 | Talk: \"An in-depth look at AnnData\" by [Ilan Gold](https://github.com/ilan-gold) |\n|                              | 10:00 – 11:30 | 1) Basic pre-processing of scRNA-seq data |\n|                              |               | 2) Batch effect correction                |\n|                              |               | 3) Downstream analysis                    |\n|                              | 11:30 - 12:00 | Hands-on coding \u0026 Troubleshooting         |\n|                              | 12:00 – 13:00 | Lunch                                     |\n|                              | 13:00 – 13:30 | Intro to \"Trajectory analysis\"            |\n|                              | 13:30 – 13:40 | Break                                     |\n|                              | 13:40 – 15:20 | Trajectory analysis                       |\n|                              | 15:20 – 15:40 | Break                                     |\n|                              | 15:40 – 17:30 | Trajectory analysis                       |\n|                              | 19:00 - tbd   | Dinner at [Porta Nova](https://www.tripadvisor.de/Restaurant_Review-g187323-d2456707-Reviews-Porta_Nova-Berlin.html) ([Robert-Koch-Platz 12](https://maps.app.goo.gl/wFXHXyAk1Fdkpf658))                           |\n|                              |               |                                           |\n| **Tuesday, 08.04.2025**      | 09:00 – 09:30 | Recap and Q\u0026A, tech setup for spatial workshop |\n|                              | 09:30 – 10:00 | Talk: \"Clonal dynamics and mitochondrial genetics through the\u003cbr\u003elens of single-cell multi-omics\" by [Leif Ludwig](https://www.mdc-berlin.de/de/person/dr-med-dr-rer-nat-leif-s-ludwig) |\n|                              | 10:00 – 11:30 | 1) Ligand-receptor interaction analysis   |\n|                              |               | 2) Differential cellular abundance        |\n|                              | 11:30 - 12:00 | Hands-on coding \u0026 Troubleshooting         |\n|                              | 12:00 – 13:00 | Lunch                                     |\n|                              | 13:00 – 13:30 | Intro to \"Spatial Omics\"                  |\n|                              | 13:30 – 13:40 | Break                                     |\n|                              | 13:40 – 15:20 | Spatial preprocessing \u0026 analysis          |\n|                              | 15:20 – 15:40 | Break                                     |\n|                              | 15:40 – 17:30 | Spatial preprocessing \u0026 analysis          |\n|                              | 20:00 - tbd   | Dinner (self-organised)                   |\n|                              |               |                                           |\n| **Wednesday, 09.042025** | 09:00 – 09:30 | Talk: “Spatiotemporal dynamics of tumor development in a novel\u003cbr\u003etriple-negative breast cancer model\" by [Tancredi Massimo Pentimalli](www.linkedin.com/in/tancredi-massimo-pentimalli) |\n|                              | 09:30 – 11:30 | Talk: \"Foxa2 pioneers enteroendocrine lineage recruitment from\u003cbr\u003eintestinal stem cells\" by [Michael Sterr](https://www.helmholtz-munich.de/en/pi-3-20)     |\n|                              | 10:00 – 11:30 | Option A) Reproduce published figures     |\n|                              |               | Option B) Discuss your own data/analysis  |\n|                              | 11:30 – 12:00 | Results / Feedback                        |\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2F202504_workshop_gscn","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2F202504_workshop_gscn","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2F202504_workshop_gscn/lists"}