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.
