Here are
33 public repositories
matching this topic...
Base Classes and Functions for Mass Spectrometry and Proteomics
Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis
Updated
Oct 17, 2021
Python
RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.
Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.
An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.
Updated
Aug 6, 2019
Jupyter Notebook
A unifying bioinformatics framework for organelle proteomics
PACOM (Proteomics Assay COMparator) is a Java stand alone tool for visualize and compare large proteomics datasets
Updated
Jul 27, 2021
Java
DeltaMass: view and interrogate open proteomics search data
Updated
Mar 31, 2021
Java
Protein Cluster Quant is a Java software for the analysis of complex proteomics samples (quantitative or not). It helps to reduce the redundancy of the peptide-to-protein relationship and to visualize the results in a bipartite network (Cytoscape).
Updated
Jul 27, 2021
Python
Molecular biology experiments, mass spectrometry-based proteomics, and reproducible data analysis in R
Updated
Jul 19, 2020
Rich Text Format
Feature extraction from .pdb files
Updated
Oct 6, 2021
Jupyter Notebook
ProXI: Schema definitions for the Proteomics eXpression Interface
Updated
Jul 30, 2020
JavaScript
Updated
Jul 1, 2020
Nextflow
protGear is a package for protein microarray data processing just before the main analysis.
Updated
Jul 21, 2021
HTML
Prediction of molecular subtypes of Breast Cancer based on TCGA proteomic data
Updated
Aug 25, 2021
HTML
Converter from DTASelect to pepXML formats
Updated
Dec 19, 2018
Java
Indexing of FASTA files for searching peptide masses and sequences
Updated
Oct 12, 2020
Java
Repository for proteomic data analysis used in the publication "Disruption of acetyl-lysine turnover in muscle mitochondria promotes insulin resistance and redox stress without overt respiratory dysfunction."
Updated
May 24, 2020
Jupyter Notebook
Custom analysis of in vitro circadian proteomics and phosphoproteomics using multiple sets of 10plex TMT with two genotypes
QC scripts for LC-MS proteomic equipment based on Proteome Discoverer 2.4 output
Updated
Aug 11, 2021
Python
General Java util classes used across different projects
Updated
Aug 11, 2021
Java
A python-based program to optimise mass spectrometer collision energies for peptides in HDX-MS experiments
Updated
Mar 6, 2021
Python
Converter from Census TMT output file to the input of MSstatsTMT
Making volcano plots from proteomic data in IgorPro
Updated
May 11, 2021
IGOR Pro
List of online databases and resources for Mycobacterium Tuberculosis
Simple workflows for the isobaric-labeling proteomic data from Proteome Discoverer with ANOVA, t-testing, DEqMS/limma and annotation via fgsea
Java API for the extraction and management of MIAPE documents from standard proteomics data files
Updated
Dec 16, 2020
Java
Parser for quantitative data from files created by Census software.
Updated
Jul 23, 2021
Java
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