SanXoT software package

Diagram showing the main modules used in the SanXoT software package.

The SanXoT software package is a bioinformatic resource made in the Cardiovascular Proteomics Lab at CNIC to build workflows for quantitative high-throughput proteomics, systems biology and the statistical analysis, integration and comparison of experiments.

Download

You can download windows standalone executables or the source code from GitHub: https://github.com/CNIC-Proteomics/SanXoT

Getting started

You can check how to use SanXoT for a general overview of the package, its design, data structure and building of workflows.

Unit test

You can check the unit tests for SanXoT or explore SanXoT features.

Programs included

For performing statistics:

• SanXoT, the central program, performing the integration of any lower level set of data, to any higher level set of data.
• SanXoTSieve, tool for detecting outliers in a SanXoT integration.
• Klibrate, calculator of the constant k for the inital calibration of data.

Systems biology specific:

• Sanson, detector of cateogories containing similar sets of proteins, showing changing proteins within each category.
• SanXoTGauss, generator of gaussian graphs associated to each category.
• Coordinometer, to calculate the degree of a coordination with given qc and ca stat files.
• Arbor, creator of Gene Ontology-like tree graphs, showing changing proteins in each category.
• Camacho, generator of relation files from text tables, especially from DAVID.
• SanXoTSqueezer, a detector of relevant categories in a systems biology analysis, filtering by FDR and number of proteins.
• Anselmo, a program to identify which integration holds the median of the variance from a set of randomised SanXoT integrations.

To integrate experiments:

• Cardenio, to generate the global relations and data files for several replicates (biological or technical) to be merged.

• For post-translational modifications:

• Trilogy, to tag peptides in relations files where non-modified peptides are used as reference in PTM analysis.

For other functions:

• MaesePedro, a tool for pseudoinverting FASTA protein databases.
• CataPep, a tool to make zero the XCorrs of all PSMs in an MSF file, excluding those provided in a white list.
• Aljamia, for parsing data between text files with tab separated tables.
• LogMasher, to collect variances from log files generated by SanXoT for a given path.

Licence

You can check at PROTEOMICA:Copyrights the licence under which all the programs presented here are available.