A collection of tools for biomedical research assay analysis in Python.
Project description
A collection of tools for biomedical research assay analysis in Python.
Key Features
Analysis for assays such as digital ELISA, 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
Getting Started
Installation
You can install waltlabtools using Anaconda (recommended) or PyPI. If you’re not comfortable with the command line, begin by installing Anaconda Navigator. Then follow these instructions 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) or pip install waltlabtools (requires pip, which should come with Python).
Dependencies
waltlabtools requires
If installing with pip or conda, numpy and scipy will be installed automatically
Specific modules have additional requirements:
waltlabtools.read (for importing data from Quanterix instruments) requires
pandas ≥ 0.25
waltlabtools also plays well with
JAX for accelerated numerical computing – waltlabtools will use jax.numpy instead of numpy if jax is loaded
JupyterLab for interactively writing code
pandas for data import/export and organization
matplotlib for plotting
scikit-learn for data analysis
All of these packages can all be installed using conda or pip.
Usage
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 for Advanced Diagnostics at Brigham and Women’s Hospital, Harvard Medical School, and the Wyss Institute for Biologically Inspired Engineering.
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