These are a couple of simple python scripts to help you navigate through PRIDE (The Proteomics Identifications Database).
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Updated
Nov 18, 2022 - Python
These are a couple of simple python scripts to help you navigate through PRIDE (The Proteomics Identifications Database).
Map the peptides to its corresponding protein sequence and locate the modification sites
Python program which is able to analyse dssp files in order to estimate the interacting area and interacting residues between monomers of a complex protein
QC scripts for LC-MS proteomic equipment based on Proteome Discoverer 2.4 output
Introduction to QFeatures, Bioconductor data object for proteomics
Scrape UniProt for functional summaries and append to table
Different python tools to validate and convert SDRF files
Peptide-based linear mixed models to assess differential gene expression in shotgun proteomics experiments
Project in the Durrant Lab at UPitt that wanted to re-use code from a previous neural network ligand-protein interaction software to extract features for ML
A collection of utility functions for processing, analysing and plotting proteomic data
Select specified scans and precursors from a mzML file
Helper scripts for crosslink analysis.
Package to study time series (or other series) multi-omics patterns of expresssion with replicates
A Python wrapper for the Chaparral API.
A python-based program to optimise mass spectrometer collision energies for peptides in HDX-MS experiments
In Silico Trypsin/Lys-C Clevage Site Prediction
A script and functions to group and validate MS Annika results.
Code used for processing proteomics data associated with the publication by Yan et al., submitted to Nature Communications in 2024
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