{"id":21962513,"url":"https://github.com/biocpy/singlecellexperiment","last_synced_at":"2025-04-23T21:24:20.309Z","repository":{"id":62592367,"uuid":"504200174","full_name":"BiocPy/SingleCellExperiment","owner":"BiocPy","description":"Container class for single-cell experiments","archived":false,"fork":false,"pushed_at":"2025-04-21T16:28:39.000Z","size":4553,"stargazers_count":7,"open_issues_count":1,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-21T17:35:41.279Z","etag":null,"topics":["singlecellexperiment"],"latest_commit_sha":null,"homepage":"https://biocpy.github.io/SingleCellExperiment/","language":"Python","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/BiocPy.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.md","dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-06-16T15:03:10.000Z","updated_at":"2025-03-11T03:03:17.000Z","dependencies_parsed_at":"2024-03-04T03:47:14.902Z","dependency_job_id":"9f699f81-8bfb-4f3a-bf57-5dc7b0077ce8","html_url":"https://github.com/BiocPy/SingleCellExperiment","commit_stats":null,"previous_names":[],"tags_count":29,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiocPy%2FSingleCellExperiment","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiocPy%2FSingleCellExperiment/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiocPy%2FSingleCellExperiment/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BiocPy%2FSingleCellExperiment/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BiocPy","download_url":"https://codeload.github.com/BiocPy/SingleCellExperiment/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250515762,"owners_count":21443480,"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":["singlecellexperiment"],"created_at":"2024-11-29T10:42:42.312Z","updated_at":"2025-04-23T21:24:20.296Z","avatar_url":"https://github.com/BiocPy.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)\n[![PyPI-Server](https://img.shields.io/pypi/v/SingleCellExperiment.svg)](https://pypi.org/project/SingleCellExperiment/)\n![Unit tests](https://github.com/BiocPy/SingleCellExperiment/actions/workflows/run-tests.yml/badge.svg)\n\n# SingleCellExperiment\n\nThis package provides container class to represent single-cell experimental data as 2-dimensional matrices. In these matrices, the rows typically denote features or genomic regions of interest, while columns represent cells. In addition, a `SingleCellExperiment` (SCE) object may contain low-dimensionality embeddings, alternative experiments performed on same sample or set of cells. Follows Bioconductor's [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html).\n\n\n## Install\n\nTo get started, install the package from [PyPI](https://pypi.org/project/singlecellexperiment/)\n\n```bash\npip install singlecellexperiment\n```\n\n## Usage\n\nThe `SingleCellExperiment` extends [RangedSummarizedExperiment](https://github.com/BiocPy/SummarizedExperiment) and contains additional attributes:\n\n- `reduced_dims`: Slot for low-dimensionality embeddings for each cell.\n- `alternative_experiments`: Manages multi-modal experiments performed on the same sample or set of cells.\n- `row_pairs` or `column_pairs`: Stores relationships between features or cells.\n\nReaders are available to parse h5ad or `AnnData` objects to SCE:\n\n```python\nimport singlecellexperiment\n\nsce = singlecellexperiment.read_h5ad(\"tests/data/adata.h5ad\")\n```\n\n    ## output\n    class: SingleCellExperiment\n    dimensions: (20, 30)\n    assays(3): ['array', 'sparse', 'X']\n    row_data columns(5): ['var_cat', 'cat_ordered', 'int64', 'float64', 'uint8']\n    row_names(0):\n    column_data columns(5): ['obs_cat', 'cat_ordered', 'int64', 'float64', 'uint8']\n    column_names(0):\n    main_experiment_name:\n    reduced_dims(0): []\n    alternative_experiments(0): []\n    row_pairs(0): []\n    column_pairs(0): []\n    metadata(2): O_recarray nested\n\n***OR construct one from scratch***\n\n```python\nfrom singlecellexperiment import SingleCellExperiment\n\ntse = SingleCellExperiment(\n    assays={\"counts\": counts}, row_data=df_gr, col_data=col_data,\n    reduced_dims={\"tsne\": ..., \"umap\": ...}, alternative_experiments={\"atac\": ...}\n)\n```\n\nSince `SingleCellExperiment` extends `RangedSummarizedExperiment`, most methods especially slicing and accessors are inherited from the parent classes.\nCheckout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.\n\n\u003c!-- pyscaffold-notes --\u003e\n\n## Note\n\nThis project has been set up using PyScaffold 4.5. For details and usage\ninformation on PyScaffold see https://pyscaffold.org/.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocpy%2Fsinglecellexperiment","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiocpy%2Fsinglecellexperiment","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocpy%2Fsinglecellexperiment/lists"}