{"id":26786881,"url":"https://github.com/marrlab/car_t_targetidentification","last_synced_at":"2025-04-19T19:34:32.653Z","repository":{"id":112116778,"uuid":"582128303","full_name":"marrlab/CAR_T_TargetIdentification","owner":"marrlab","description":"Computational identification of targets for CAR-T cell therapy in AML","archived":false,"fork":false,"pushed_at":"2022-12-25T20:40:49.000Z","size":46670,"stargazers_count":16,"open_issues_count":2,"forks_count":3,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-03-29T12:17:03.247Z","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/marrlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"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}},"created_at":"2022-12-25T19:47:20.000Z","updated_at":"2024-12-18T22:55:39.000Z","dependencies_parsed_at":null,"dependency_job_id":"292d9adc-a0f3-48da-bd6f-84c2fea5fc35","html_url":"https://github.com/marrlab/CAR_T_TargetIdentification","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marrlab%2FCAR_T_TargetIdentification","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marrlab%2FCAR_T_TargetIdentification/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marrlab%2FCAR_T_TargetIdentification/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/marrlab%2FCAR_T_TargetIdentification/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/marrlab","download_url":"https://codeload.github.com/marrlab/CAR_T_TargetIdentification/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249780495,"owners_count":21324558,"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":"2025-03-29T12:17:08.291Z","updated_at":"2025-04-19T19:34:32.646Z","avatar_url":"https://github.com/marrlab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Computational identification of targets for CAR-T cell therapy in AML\n\nThis repository contains all jupyter notebooks to reproduce the results of the single-cell data analysis from: \n\nA. Gottschlich, M. Thomas, R. Grünmeier et al., \"Single-cell transcriptomic atlas-guided development of chimeric antigen-receptor (CAR) T cells for the treatment of acute myeloid leukemia\", Nature Biotechnology (2023).\n\nThe notebooks contain code for the following analyses:\n\n- Preprocessing and Analysis of AML datasets including query to reference mapping\n- Preprocessing and harmonization of single cell data across multiple organs using public datasets\n- Combining public databases to infer genes coding for surface- and druggable proteins as well as analysis of bulk sequencing data\n\nNote that the analysis was done in python 3 using ```scanpy``` v.1.4.6 to 1.9.1 and ```anndata``` v.0.7.1 to 0.8.0 unless otherwise stated. Some functions may have changed when using other package versions. \nAdditionally, ```numpy``` (v. 1.18.2+), ```pandas``` (v. 1.3.5+) and ```scipy``` (v. 1.4.1+) are required. Numeric results can vary depending on package versions and e.g. minor results. All scRNA-seq figures were plotted using ```matplotlib``` and ```seaborn```. \n\n\nIf the materials in this repository are of use to you, please consider citing the above publication.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarrlab%2Fcar_t_targetidentification","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmarrlab%2Fcar_t_targetidentification","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarrlab%2Fcar_t_targetidentification/lists"}