Difference between revisions of "SanXoT software package"
(Created page with "The '''SanXoT software package''' is a bioinformatic resource made in the Cardiovascular Proteomics Lab at CNIC to build workflows for quantitative high-throughput proteomics,...") |
(→Getting started) |
||
| (14 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| + | [[File:SanXoT main modules.png|thumb|600px|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. | 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 https://github.com/CNIC-Proteomics/SanXoT]''' | ||
| + | |||
| + | == Getting started == | ||
| + | |||
| + | You can check '''[[How to use SanXoT|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 '''[[exploring SanXoT features|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. | ||
| + | |||
| + | [[Category:SanXoT software package]] | ||
Latest revision as of 11:47, 8 August 2018
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.
