celloracle


Namecelloracle JSON
Version 0.20.0 PyPI version JSON
download
home_pagehttps://github.com/morris-lab/CellOracle
Summaryin silico gene perturbation analysis and GRN analysis with single cell data
upload_time2024-11-15 03:54:07
maintainerNone
docs_urlNone
authorKenji Kamimoto
requires_python>=3.6
licenseApache License Version 2.0
keywords scrna-seq grn simulation gene perturbation
VCS
bugtrack_url
requirements numpy scipy cython numba matplotlib seaborn scikit-learn h5py pandas velocyto umap-learn pyarrow tqdm igraph louvain jupyter anndata scanpy joblib goatools genomepy gimmemotifs anndata
Travis-CI No Travis.
coveralls test coverage No coveralls.
            CellOracle
==========

|GitHub Workflow Status| |PyPI| |PyPI - Python Version| |PyPI - Wheel|
|Downloads| |Docker Pulls|

CellOracle is a python library for in silico gene perturbation analyses
using single-cell omics data and Gene Regulatory Network models.

For more information, please read our paper: `Dissecting cell identity
via network inference and in silico gene
perturbation <https://www.nature.com/articles/s41586-022-05688-9>`__.

Documentation, Codes, and Tutorials
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CellOracle documentation is available through the link below.

`Web
documentation <https://morris-lab.github.io/CellOracle.documentation/>`__

Questions and errors
~~~~~~~~~~~~~~~~~~~~

If you have a question, error, bug, or problem, please use the `Github
issue page <https://github.com/morris-lab/CellOracle/issues>`__.

Supported Species and reference genomes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-  Human: [‘hg38’, ‘hg19’]
-  Mouse: [‘mm39’, ‘mm10’, ‘mm9’]
-  S.cerevisiae: [“sacCer2”, “sacCer3”]
-  Zebrafish: [“danRer7”, “danRer10”, “danRer11”]
-  Xenopus tropicalis: [“xenTro2”, “xenTro3”]
-  Xenopus laevis: [“Xenopus_laevis_v10.1”]
-  Rat: [“rn4”, “rn5”, “rn6”]
-  Drosophila: [“dm3”, “dm6”]
-  C.elegans: [“ce6”, “ce10”]
-  Arabidopsis: [“TAIR10”]
-  Chicken: [“galGal4”, “galGal5”, “galGal6”]
-  Guinea Pig: [“Cavpor3.0”]
-  Pig: [“Sscrofa11.1”]

Changelog
~~~~~~~~~

Please go to `this
page <https://morris-lab.github.io/CellOracle.documentation/changelog/index.html>`__.

.. |GitHub Workflow Status| image:: https://img.shields.io/github/actions/workflow/status/morris-lab/CellOracle/build_check.yml?branch=master
   :target: https://github.com/morris-lab/CellOracle/actions/workflows/build_check.yml
.. |PyPI| image:: https://img.shields.io/pypi/v/celloracle?color=blue
   :target: https://pypi.org/project/celloracle/
.. |PyPI - Python Version| image:: https://img.shields.io/pypi/pyversions/celloracle
   :target: https://pypi.org/project/celloracle/
.. |PyPI - Wheel| image:: https://img.shields.io/pypi/wheel/celloracle
   :target: https://pypi.org/project/celloracle/
.. |Downloads| image:: https://static.pepy.tech/personalized-badge/celloracle?period=total&units=international_system&left_color=grey&right_color=orange&left_text=Downloads
   :target: https://pepy.tech/project/celloracle
.. |Docker Pulls| image:: https://img.shields.io/docker/pulls/kenjikamimoto126/celloracle_ubuntu?color=red
   :target: https://hub.docker.com/r/kenjikamimoto126/celloracle_ubuntu

            

Raw data

            {
    "_id": null,
    "home_page": "https://github.com/morris-lab/CellOracle",
    "name": "celloracle",
    "maintainer": null,
    "docs_url": null,
    "requires_python": ">=3.6",
    "maintainer_email": null,
    "keywords": "scRNA-seq, GRN, simulation, gene perturbation",
    "author": "Kenji Kamimoto",
    "author_email": "kamimoto@wustl.edu",
    "download_url": "https://files.pythonhosted.org/packages/35/e9/35a130e138c5defc6ace102e12fa98c81e02f0e2f1baa168af4f98106acd/celloracle-0.20.0.tar.gz",
    "platform": null,
    "description": "CellOracle\n==========\n\n|GitHub Workflow Status| |PyPI| |PyPI - Python Version| |PyPI - Wheel|\n|Downloads| |Docker Pulls|\n\nCellOracle is a python library for in silico gene perturbation analyses\nusing single-cell omics data and Gene Regulatory Network models.\n\nFor more information, please read our paper: `Dissecting cell identity\nvia network inference and in silico gene\nperturbation <https://www.nature.com/articles/s41586-022-05688-9>`__.\n\nDocumentation, Codes, and Tutorials\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nCellOracle documentation is available through the link below.\n\n`Web\ndocumentation <https://morris-lab.github.io/CellOracle.documentation/>`__\n\nQuestions and errors\n~~~~~~~~~~~~~~~~~~~~\n\nIf you have a question, error, bug, or problem, please use the `Github\nissue page <https://github.com/morris-lab/CellOracle/issues>`__.\n\nSupported Species and reference genomes\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n-  Human: [\u2018hg38\u2019, \u2018hg19\u2019]\n-  Mouse: [\u2018mm39\u2019, \u2018mm10\u2019, \u2018mm9\u2019]\n-  S.cerevisiae: [\u201csacCer2\u201d, \u201csacCer3\u201d]\n-  Zebrafish: [\u201cdanRer7\u201d, \u201cdanRer10\u201d, \u201cdanRer11\u201d]\n-  Xenopus tropicalis: [\u201cxenTro2\u201d, \u201cxenTro3\u201d]\n-  Xenopus laevis: [\u201cXenopus_laevis_v10.1\u201d]\n-  Rat: [\u201crn4\u201d, \u201crn5\u201d, \u201crn6\u201d]\n-  Drosophila: [\u201cdm3\u201d, \u201cdm6\u201d]\n-  C.elegans: [\u201cce6\u201d, \u201cce10\u201d]\n-  Arabidopsis: [\u201cTAIR10\u201d]\n-  Chicken: [\u201cgalGal4\u201d, \u201cgalGal5\u201d, \u201cgalGal6\u201d]\n-  Guinea Pig: [\u201cCavpor3.0\u201d]\n-  Pig: [\u201cSscrofa11.1\u201d]\n\nChangelog\n~~~~~~~~~\n\nPlease go to `this\npage <https://morris-lab.github.io/CellOracle.documentation/changelog/index.html>`__.\n\n.. |GitHub Workflow Status| image:: https://img.shields.io/github/actions/workflow/status/morris-lab/CellOracle/build_check.yml?branch=master\n   :target: https://github.com/morris-lab/CellOracle/actions/workflows/build_check.yml\n.. |PyPI| image:: https://img.shields.io/pypi/v/celloracle?color=blue\n   :target: https://pypi.org/project/celloracle/\n.. |PyPI - Python Version| image:: https://img.shields.io/pypi/pyversions/celloracle\n   :target: https://pypi.org/project/celloracle/\n.. |PyPI - Wheel| image:: https://img.shields.io/pypi/wheel/celloracle\n   :target: https://pypi.org/project/celloracle/\n.. |Downloads| image:: https://static.pepy.tech/personalized-badge/celloracle?period=total&units=international_system&left_color=grey&right_color=orange&left_text=Downloads\n   :target: https://pepy.tech/project/celloracle\n.. |Docker Pulls| image:: https://img.shields.io/docker/pulls/kenjikamimoto126/celloracle_ubuntu?color=red\n   :target: https://hub.docker.com/r/kenjikamimoto126/celloracle_ubuntu\n",
    "bugtrack_url": null,
    "license": "Apache License Version 2.0",
    "summary": "in silico gene perturbation analysis and GRN analysis with single cell data",
    "version": "0.20.0",
    "project_urls": {
        "Homepage": "https://github.com/morris-lab/CellOracle"
    },
    "split_keywords": [
        "scrna-seq",
        " grn",
        " simulation",
        " gene perturbation"
    ],
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "337c11f7ccb68d0f601e5eb7b7f836503d48044a8f2cbbf351021eae7f05d9d6",
                "md5": "46c46fd9085a1ff7bc4916d97477992a",
                "sha256": "b0d82ce72e77476ca1a79a2b555f70bde86b39dcd56f154f1f1dc678a5fabacf"
            },
            "downloads": -1,
            "filename": "celloracle-0.20.0-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "46c46fd9085a1ff7bc4916d97477992a",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": ">=3.6",
            "size": 12372319,
            "upload_time": "2024-11-15T03:54:02",
            "upload_time_iso_8601": "2024-11-15T03:54:02.567931Z",
            "url": "https://files.pythonhosted.org/packages/33/7c/11f7ccb68d0f601e5eb7b7f836503d48044a8f2cbbf351021eae7f05d9d6/celloracle-0.20.0-py3-none-any.whl",
            "yanked": false,
            "yanked_reason": null
        },
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "35e935a130e138c5defc6ace102e12fa98c81e02f0e2f1baa168af4f98106acd",
                "md5": "d5eedea24c20ab1fc8f35f9c0298fa66",
                "sha256": "a7d57a14c2b8cd2d81abb6cf141829ef85013f298c9a36560b096fbddcbce7a2"
            },
            "downloads": -1,
            "filename": "celloracle-0.20.0.tar.gz",
            "has_sig": false,
            "md5_digest": "d5eedea24c20ab1fc8f35f9c0298fa66",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=3.6",
            "size": 12181984,
            "upload_time": "2024-11-15T03:54:07",
            "upload_time_iso_8601": "2024-11-15T03:54:07.450909Z",
            "url": "https://files.pythonhosted.org/packages/35/e9/35a130e138c5defc6ace102e12fa98c81e02f0e2f1baa168af4f98106acd/celloracle-0.20.0.tar.gz",
            "yanked": false,
            "yanked_reason": null
        }
    ],
    "upload_time": "2024-11-15 03:54:07",
    "github": true,
    "gitlab": false,
    "bitbucket": false,
    "codeberg": false,
    "github_user": "morris-lab",
    "github_project": "CellOracle",
    "travis_ci": false,
    "coveralls": false,
    "github_actions": true,
    "requirements": [
        {
            "name": "numpy",
            "specs": [
                [
                    "==",
                    "1.26.4"
                ]
            ]
        },
        {
            "name": "scipy",
            "specs": []
        },
        {
            "name": "cython",
            "specs": []
        },
        {
            "name": "numba",
            "specs": [
                [
                    ">=",
                    "0.50.1"
                ]
            ]
        },
        {
            "name": "matplotlib",
            "specs": [
                [
                    "<",
                    "3.7"
                ]
            ]
        },
        {
            "name": "seaborn",
            "specs": []
        },
        {
            "name": "scikit-learn",
            "specs": []
        },
        {
            "name": "h5py",
            "specs": [
                [
                    ">=",
                    "3.1.0"
                ]
            ]
        },
        {
            "name": "pandas",
            "specs": [
                [
                    ">=",
                    "1.0.3"
                ],
                [
                    "<=",
                    "1.5.3"
                ]
            ]
        },
        {
            "name": "velocyto",
            "specs": [
                [
                    ">=",
                    "0.17"
                ]
            ]
        },
        {
            "name": "umap-learn",
            "specs": []
        },
        {
            "name": "pyarrow",
            "specs": [
                [
                    ">=",
                    "0.17"
                ]
            ]
        },
        {
            "name": "tqdm",
            "specs": [
                [
                    ">=",
                    "4.45"
                ]
            ]
        },
        {
            "name": "igraph",
            "specs": [
                [
                    ">=",
                    "0.10.1"
                ]
            ]
        },
        {
            "name": "louvain",
            "specs": []
        },
        {
            "name": "jupyter",
            "specs": []
        },
        {
            "name": "anndata",
            "specs": [
                [
                    ">=",
                    "0.7.5"
                ]
            ]
        },
        {
            "name": "scanpy",
            "specs": [
                [
                    ">=",
                    "1.6"
                ]
            ]
        },
        {
            "name": "joblib",
            "specs": []
        },
        {
            "name": "goatools",
            "specs": []
        },
        {
            "name": "genomepy",
            "specs": [
                [
                    ">=",
                    "0.8.4"
                ]
            ]
        },
        {
            "name": "gimmemotifs",
            "specs": [
                [
                    "<=",
                    "0.17.2"
                ],
                [
                    ">=",
                    "0.14.4"
                ]
            ]
        },
        {
            "name": "anndata",
            "specs": [
                [
                    "<=",
                    "0.10.8"
                ]
            ]
        }
    ],
    "lcname": "celloracle"
}
        
Elapsed time: 1.22322s