ace-elispot 0.1.0.6

ELISpot configuration generation and pool spot count deconvolution

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)

Operating System	Link	Version
Mac	Download	v0.1.0.5 (latest)
Windows	Download	v0.1.0.5 (latest)

Previous versions of ACE are available here.

01-2. Python Package

ACE is also available as a python package. Download the latest stable release version from here.
Subsequently install the ACE package using pip:

pip install ace-<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
  --version, -v         show program's 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.