waltlabtools¶
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_quanterix (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.