This package has moved to https://github.com/biocircuits/murraylab_tools and is no longer actively maintained here.
Code for common tasks in the Murray lab. Supports Python >=3.6 only.
Install with the following (probably requires sudo): pip install git+git://github.com/biocircuits/murraylab_tools.git@master
To update, run (also with superuser privilege): pip install --upgrade --no-deps git+git://github.com/biocircuits/murraylab_tools.git@master
Currently includes the following subpackages:
- A code block that will automatically text or email you when your code is done running.
echo: Echo Setup for TX-TL Experiments (and others) =============================================
Code to produce Echo source plate setup instructions and picklists for one of the following cases:
- A TX-TL experiment with a TX-TL setup spreadsheet.
- Programmatically-constructed TX-TL experiments, including easy 2D dilution series setup plus arbitrary additions.
- Fully general well contents, as defined by a spreadsheet of source materials and a spreadsheet listing what goes in each.
For details, see the "Echo Setup Usage Examples" ipython notebook under "examples".
Code for converting raw excel/CSV data from a Biotek plate reader into tidy format, plus a class to make plotting Biotek data traces quick and easy (BiotekCellPlotter).
Also contains convenience functions for analysis of Biotek timecourse data:
- Fluorescence calibration against lab data (TX-TL data only)
- Background subtraction
- Endpoint averaging
- Data smoothing (spline fit or moving average)
- Smoothed derivative calculation
- OD normalization
- Growth curve summarazation with logistic curve fits
For details, see the "Biotek Analysis Usage Examples" ipython notebook under "examples".