Combined Open and Narrow searches via Group Analysis
Project description
CONGA is a tool for discovering peptides in mass spectrometry data with rigourous FDR control. It is designed to allow for unexpected post-translational modifications as well as chimeric spectra. Open Group-walk takes three inputs: (1) the set of top-scoring PSMs from a traditional, narrow-window search against a concatenated target-decoy database, (2) the set of top-k PSMs (or fewer if less than k PSMs exist) from an open search, again against a concatenated target-decoy database, and (3) the pairs of target and decoy peptide sequences from the database. Given this, Open Group-walk will return a discovery list of peptides.
Documentation
You can find documentation on how to use CONGA over on readtheddocs. Alternatively you can find the same documentation under docs/pages in this respository.
Paper
A link to the biorXiv paper will eventually go here.
Installation
To install, first create a virtual environment using conda:
conda create --name conga_env python=3.9
Then activate this virtual environment:
conda activate conga_env
Next download the latest release using pip:
pip install CONGA
Alternatively you can download the latest release from Github, and install using pip in the same directory as setup.py using:
pip install .
Please see the documentation, specifically the tutorial, on how to run CONGA.
Releasing
Releases are published automatically when a tag is pushed to GitHub.
# Set next version number
export RELEASE=x.x.x
# Create tags
git commit --allow-empty -m "Release $RELEASE"
git tag -a $RELEASE -m "Version $RELEASE"
# Push
git push upstream --tags
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