waltlabtools
============
.. image:: https://img.shields.io/conda/vn/tylerdougan/waltlabtools?label=Anaconda
:target: https://anaconda.org/tylerdougan/waltlabtools
:alt: Conda
.. image:: https://img.shields.io/pypi/v/waltlabtools?label=PyPI
:target: https://pypi.org/project/waltlabtools
:alt: PyPI
.. image:: https://img.shields.io/readthedocs/waltlabtools?label=Documentation
:target: https://waltlabtools.readthedocs.io/en/latest/
:alt: Documentation
.. image:: https://img.shields.io/github/repo-size/tylerdougan/waltlabtools?label=GitHub
:target: https://github.com/tylerdougan/waltlabtools
:alt: GitHub
A collection of tools for biomedical research assay analysis in Python.
Key Features
------------
- Analysis for assays such as
`digital ELISA <http://www.ncbi.nlm.nih.gov/pmc/articles/pmc2919230/>`__,
including single-molecule array (Simoa) assays
- Read instrument-generated files and calculate calibration curves,
concentrations, limits of detection, and more
- Free and open-source software under the
`GNU General Public License v3 <https://www.gnu.org/licenses/gpl-3.0.en.html>`__
Getting Started
---------------
Installation
^^^^^^^^^^^^
You can install waltlabtools using
`Anaconda <https://anaconda.org/tylerdougan/waltlabtools>`__ (recommended) or
`PyPI <https://pypi.org/project/waltlabtools/>`__. If you're not comfortable
with the command line, begin by installing
`Anaconda Navigator <https://www.anaconda.com/products/individual>`__. Then follow
`these instructions <https://docs.anaconda.com/anaconda/navigator/tutorials/manage-channels/>`__
to add the channel ``tylerdougan``, and install waltlabtools from this channel.
Alternatively, install waltlabtools from the command line with
``conda install -c tylerdougan waltlabtools`` (recommended; requires you to
first install Anaconda or
`Miniconda <https://docs.conda.io/en/latest/miniconda.html>`__) or
``pip install waltlabtools`` (requires
`pip <https://pip.pypa.io/en/stable/getting-started/>`__, which should come
with Python).
Dependencies
^^^^^^^^^^^^
- waltlabtools requires
- `numpy <https://numpy.org/doc/stable/index.html>`__ ≥ 1.10
- `scipy <https://docs.scipy.org/doc/scipy/getting_started.html>`__ ≥ 1.3
- If installing with pip or conda, numpy and scipy will be installed
automatically
- Specific modules have additional requirements:
- `waltlabtools.read <https://waltlabtools.readthedocs.io/en/latest/waltlabtools.read.html>`__
(for importing data from Quanterix instruments) requires
- `pandas <https://pandas.pydata.org>`__ ≥ 0.25
- waltlabtools also plays well with
- `JAX <https://jax.readthedocs.io/en/latest/index.html>`__
for accelerated numerical computing – waltlabtools will use jax.numpy
instead of numpy if jax is loaded
- `JupyterLab <https://jupyterlab.readthedocs.io/en/stable/>`__
for interactively writing code
- `pandas <https://pandas.pydata.org>`__
for data import/export and organization
- `matplotlib <https://matplotlib.org>`__ for plotting
- `scikit-learn <https://scikit-learn.org/stable/>`__ for data analysis
All of these packages can all be installed using
`conda <https://docs.conda.io/projects/conda/en/latest/user-guide/install/download.html>`__
or `pip <https://pypi.org>`__.
Usage
^^^^^
.. code-block:: python
import waltlabtools as wlt # waltlabtools main functionality
import waltlabtools.read_quanterix # if using a Quanterix instrument
-----
Development of waltlabtools is led by the
`Walt Lab <https://waltlab.bwh.harvard.edu>`__ for Advanced Diagnostics
at `Brigham and Women's Hospital <https://www.brighamandwomens.org>`__,
`Harvard Medical School <https://hms.harvard.edu>`__, and the
`Wyss Institute for Biologically Inspired Engineering <https://wyss.harvard.edu>`__.
Raw data
{
"_id": null,
"home_page": "https://github.com/tylerdougan/waltlabtools",
"name": "waltlabtools",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.6",
"maintainer_email": "",
"keywords": "python,numpy,modeling,curve-fitting,diagnostics,biomedical-data-science,calibration-curve,assay,elisa,concentrations",
"author": "Tyler Dougan",
"author_email": "tyler_dougan@hst.harvard.edu",
"download_url": "https://files.pythonhosted.org/packages/fe/79/f27270767b4fda5809276c002c306a4166675c9e071b2de172020a59f1f7/waltlabtools-0.5.5.tar.gz",
"platform": "",
"description": "waltlabtools\n============\n\n.. image:: https://img.shields.io/conda/vn/tylerdougan/waltlabtools?label=Anaconda\n :target: https://anaconda.org/tylerdougan/waltlabtools\n :alt: Conda\n.. image:: https://img.shields.io/pypi/v/waltlabtools?label=PyPI\n :target: https://pypi.org/project/waltlabtools\n :alt: PyPI\n.. image:: https://img.shields.io/readthedocs/waltlabtools?label=Documentation\n :target: https://waltlabtools.readthedocs.io/en/latest/\n :alt: Documentation\n.. image:: https://img.shields.io/github/repo-size/tylerdougan/waltlabtools?label=GitHub\n :target: https://github.com/tylerdougan/waltlabtools\n :alt: GitHub\n\n\nA collection of tools for biomedical research assay analysis in Python.\n\nKey Features\n------------\n\n- Analysis for assays such as\n `digital ELISA <http://www.ncbi.nlm.nih.gov/pmc/articles/pmc2919230/>`__,\n including single-molecule array (Simoa) assays\n- Read instrument-generated files and calculate calibration curves,\n concentrations, limits of detection, and more\n- Free and open-source software under the\n `GNU General Public License v3 <https://www.gnu.org/licenses/gpl-3.0.en.html>`__\n\nGetting Started\n---------------\n\nInstallation\n^^^^^^^^^^^^\n\nYou can install waltlabtools using\n`Anaconda <https://anaconda.org/tylerdougan/waltlabtools>`__ (recommended) or\n`PyPI <https://pypi.org/project/waltlabtools/>`__. If you're not comfortable\nwith the command line, begin by installing\n`Anaconda Navigator <https://www.anaconda.com/products/individual>`__. Then follow\n`these instructions <https://docs.anaconda.com/anaconda/navigator/tutorials/manage-channels/>`__\nto add the channel ``tylerdougan``, and install waltlabtools from this channel.\n\nAlternatively, install waltlabtools from the command line with\n``conda install -c tylerdougan waltlabtools`` (recommended; requires you to\nfirst install Anaconda or\n`Miniconda <https://docs.conda.io/en/latest/miniconda.html>`__) or\n``pip install waltlabtools`` (requires\n`pip <https://pip.pypa.io/en/stable/getting-started/>`__, which should come\nwith Python).\n\n\nDependencies\n^^^^^^^^^^^^\n\n- waltlabtools requires\n\n - `numpy <https://numpy.org/doc/stable/index.html>`__ \u2265 1.10\n\n - `scipy <https://docs.scipy.org/doc/scipy/getting_started.html>`__ \u2265 1.3\n \n- If installing with pip or conda, numpy and scipy will be installed\n automatically\n\n- Specific modules have additional requirements:\n\n - `waltlabtools.read <https://waltlabtools.readthedocs.io/en/latest/waltlabtools.read.html>`__\n (for importing data from Quanterix instruments) requires\n\n - `pandas <https://pandas.pydata.org>`__ \u2265 0.25\n\n- waltlabtools also plays well with\n\n - `JAX <https://jax.readthedocs.io/en/latest/index.html>`__\n for accelerated numerical computing \u2013 waltlabtools will use jax.numpy\n instead of numpy if jax is loaded\n\n - `JupyterLab <https://jupyterlab.readthedocs.io/en/stable/>`__\n for interactively writing code\n\n - `pandas <https://pandas.pydata.org>`__\n for data import/export and organization\n\n - `matplotlib <https://matplotlib.org>`__ for plotting\n\n - `scikit-learn <https://scikit-learn.org/stable/>`__ for data analysis\n\nAll of these packages can all be installed using\n`conda <https://docs.conda.io/projects/conda/en/latest/user-guide/install/download.html>`__\nor `pip <https://pypi.org>`__.\n\n\nUsage\n^^^^^\n\n.. code-block:: python\n \n import waltlabtools as wlt # waltlabtools main functionality\n import waltlabtools.read_quanterix # if using a Quanterix instrument\n\n-----\n\n\nDevelopment of waltlabtools is led by the\n`Walt Lab <https://waltlab.bwh.harvard.edu>`__ for Advanced Diagnostics\nat `Brigham and Women's Hospital <https://www.brighamandwomens.org>`__,\n`Harvard Medical School <https://hms.harvard.edu>`__, and the\n`Wyss Institute for Biologically Inspired Engineering <https://wyss.harvard.edu>`__.\n\n\n",
"bugtrack_url": null,
"license": "GNU General Public License v3 (GPLv3)",
"summary": "A collection of tools for biomedical research assay analysis in Python.",
"version": "0.5.5",
"project_urls": {
"Bug Tracker": "https://github.com/tylerdougan/waltlabtools/issues",
"Conda": "https://anaconda.org/tylerdougan/waltlabtools",
"Documentation": "https://waltlabtools.readthedocs.io/README.html",
"Download": "https://pypi.org/project/waltlabtools/#files",
"Homepage": "https://github.com/tylerdougan/waltlabtools"
},
"split_keywords": [
"python",
"numpy",
"modeling",
"curve-fitting",
"diagnostics",
"biomedical-data-science",
"calibration-curve",
"assay",
"elisa",
"concentrations"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "ad6956abf9ee6d0b3a2989ebf238c15ca0670ea0a83f255cc391c3237284e7c4",
"md5": "bfb814fe37bb898846c841411ac96c39",
"sha256": "680c2d50b2a68673bd6c97e6a5cc9cd4e641a688128c67951c44ab29b2f108c6"
},
"downloads": -1,
"filename": "waltlabtools-0.5.5-py3-none-any.whl",
"has_sig": false,
"md5_digest": "bfb814fe37bb898846c841411ac96c39",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.6",
"size": 38155,
"upload_time": "2022-02-08T03:36:15",
"upload_time_iso_8601": "2022-02-08T03:36:15.376565Z",
"url": "https://files.pythonhosted.org/packages/ad/69/56abf9ee6d0b3a2989ebf238c15ca0670ea0a83f255cc391c3237284e7c4/waltlabtools-0.5.5-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "fe79f27270767b4fda5809276c002c306a4166675c9e071b2de172020a59f1f7",
"md5": "adce5432aa98a7f8a0e1f84a0758571f",
"sha256": "4feb605bd5851b976f2ba21923d07171de93a4c99c57f5ef016d776865735361"
},
"downloads": -1,
"filename": "waltlabtools-0.5.5.tar.gz",
"has_sig": false,
"md5_digest": "adce5432aa98a7f8a0e1f84a0758571f",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.6",
"size": 36014,
"upload_time": "2022-02-08T03:36:16",
"upload_time_iso_8601": "2022-02-08T03:36:16.825497Z",
"url": "https://files.pythonhosted.org/packages/fe/79/f27270767b4fda5809276c002c306a4166675c9e071b2de172020a59f1f7/waltlabtools-0.5.5.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2022-02-08 03:36:16",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "tylerdougan",
"github_project": "waltlabtools",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"lcname": "waltlabtools"
}
JSON
