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Releases: JacksonBurns/Crow

Crow

31 Jul 19:29
@JacksonBurns JacksonBurns
v1.1.1-WIN
b0e6de2
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Crow

  1. Minor bug fixes in PrePull

  2. Add option to keep retention times when exporting data with pre-pull

This version is intended for use on Windows operating systems, though it will function almost perfectly on Unix based operating systems with only a handful of UI errors inherent to tkinter. Please see v1.1.1-OSX for Unix-based operating systems.

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Crow

31 Jul 19:30
@JacksonBurns JacksonBurns
v1.1.1-OSX
4126950
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Crow

  1. Minor bug fixes in PrePull

  2. Add option to keep retention times when exporting data with pre-pull

This version is intended for use on Unix-based operating systems, though it will function almost perfectly on Windows with only a handful of UI errors inherent to tkinter. Please see v1.1.1-WIN for Windows.

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Crow

29 Jul 00:40
@JacksonBurns JacksonBurns
1.1.0
96d227a
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Crow

Configuration of Crow for machine specific implementations simplified via creation of a config file. Addition of features to customize how Crow picks peaks when it encounters multiple viable eluates in a well.

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Crow

10 Feb 02:12
@JacksonBurns JacksonBurns
1.0.0
327244d
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Crow

Crow

Crow Really Outta Work

What is Crow?

Crow is a software package for retrieving, diagnosing, and presenting High Throughput Experimentation data from various instruments.

Crow has three tabs: Pre-Pull, Pull, and Present. Pre-Pull identifies all peaks (and their areas) present in a given data set and generates a histogram of elution times. This is intended to help the user decide on a retention time (and small tolerance window) for each eluate to be pulled from the instrument data. With the help of Pre-Pull, Pull enables users to apidly retrieve the peak areas for large datasets and export them to an Excel file (.csv) for easy manipulation. Present takes Excel files including only the data to be placed in the pie charts, which can then be filtered in a variety of ways to better represent multivariate data.

Designed by Jackson Burns at the University of Delaware Donald Watson Lab in 2019, coded in Python in 2020.

How to use Crow

Please see this video for instructions:
https://www.jacksonwarnerburns.com/crow

Setup

Data is retrieved by parsing XML files output by the software on the High Throughput Experimentation instrument. For example, our setup uses an Agilent GC and their software to run experiments and calculate eluate peak areas.

A conda environment file (.yml) lists the required packages and versions needed to run Crow.

To configure Crow to work for your setup, there are a few small changes to make in globals_GC.py:

  • change the rawdatapath variable to the filepath of a local/network location where data files are stored
  • change the exportdatapath variable to the filepath where data files created by Pull should be saved

The indexing of the XML files in Pull_GC.py line 48 is built around our lab's particular GC and its configuration. Change this to match the location of the peak data in your particular instrument's output files.

Support

If you need help with setting up Crow, finding out how to retrieve data from your HTE instrument, or you find this program at all helpful, send me a message here: jburnsky@udel.edu with the subject line "Crow" and your name.

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