ELISpot configuration generation and pool spot count deconvolution
Project description
ACE Configurator for ELISpot
ACE facilitates (1) generation of ELISpot configurations (peptide-pool assignments) using a deep learning approach to cluster similar peptides and (2) deconvolution of pool spot counts for identification of immunogenic peptides.
01. Installation
01-1. Standalone Graphical User Interface (Recommended)
Please note that the ACE GUI software will take a long time to load (~30 seconds :coffee:). We also recommend that you have Google Chrome installed on your machine.
Operating System | Link | Version |
---|---|---|
Mac | Download | v0.1.1.0 (latest) |
Windows 10 | Download | v0.1.1.0 (latest) |
For Windows versions, first unzip the file and look for an application file called ACE
inside the unzipped foler.
Previous versions of ACE are available here.
01-2. Python Package
ACE is available on PyPI
pip install ace-elispot
You can also download a specific version of ACE from here.
Subsequently install the ACE package using pip:
pip install ace-elispot-<version>.tar.gz
Dependencies
- python3 (>= 3.10)
- pandas (>=1.5.2)
- numpy (>=1.23.1)
- ortools (9.3.10497)
- torch
- transformers (==4.30.2)
- scikit-learn
- openpyxl
- golfy (>=2.5.0)
- levenshtein
02. Usage
ACE is available as a command-line interface after you install the python package:
usage: ace [-h] [--version] {generate,deconvolve,verify} ...
ACE Configurator for ELISpot.
positional arguments:
{generate,deconvolve,verify}
ACE sub-commands.
generate Generates an ELISpot experiment configuration.
deconvolve Deconvolve hit peptide IDs given read-outs from an ELISpot experiment.
verify Verifies whether an ELISpot assignment satisfies all ACE constraints.
options:
-h, --help show this help message and exit
-v, --version show program version number and exit
Read the full documentation on the python package at https://pirl-unc.github.io/ace/
03. Citation
If you use ACE in a publication, please cite our preprint describing ACE.
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