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Welcome to the Deuteros Wiki!

These pages are designed to document some of the main features of Deuteros, as well as explain how to use certain parts.

Tutorial files

The files used for the tutorial can be found in the main Deuteros 2.0 repo, or downloaded as the source code with any of the releases.

It contains the following files:

example_data
├── example_inputs
│   ├── XylE_cluster_example.csv
│   ├── back_exchange_example.csv
│   └── HDExaminer_example.csv
├── example_output
│   ├── HDExaminer_example_dynamx.csv
│   ├── XylE_cluster_example_Table_FilteredPeptides.csv
│   ├── XylE_cluster_example_Table_RawCluster.csv
│   ├── XylE_cluster_example_Table_RemovedPeptides.csv
│   ├── XylE_cluster_example_Table_difference.csv
│   ├── XylE_cluster_example_advanced_Woods Differential_PyMOL.pml
│   ├── XylE_cluster_example_coverage_output_PyMOL.pml
│   ├── cluster_advanced_Woods Differential_Chimera_0.5.py
│   ├── cluster_advanced_Woods Differential_Chimera_30.py
│   ├── cluster_advanced_Woods Differential_Chimera_5.py
│   ├── cluster_advanced_Woods Differential_PyMOL.pml
│   ├── cluster_coverage_XylE E397Q_Chimera.py
│   ├── cluster_coverage_XylE WT_Chimera.py
│   ├── cluster_coverage_common_Chimera.py
│   ├── cluster_coverage_output_PyMOL.pml
│   ├── cluster_redundancy_XylE E397Q_Chimera.py
│   ├── cluster_redundancy_XylE WT_Chimera.py
│   └── cluster_redundancy_common_Chimera.py
└── plots
    ├── XylE_cluster_example_XYLE_ECOLI_Butterfly Differential.svg
    ├── XylE_cluster_example_XYLE_ECOLI_Coverage.svg
    ├── XylE_cluster_example_XYLE_ECOLI_Redundancy.svg
    ├── XylE_cluster_example_XYLE_ECOLI_Volcano.svg
    └── XylE_cluster_example_XYLE_ECOLI_Woods Differential.svg

Example Inputs

Example inputs contain the the input files:

• XylE_cluster_example.csv used for Tutorial 1 which shows how to import DynamX cluster files into Deuteros
• back_exchange_example.csv used for Tutorial 5 which covers back exchange
• HDExaminer_example.csv used for Tutorial 6 which shows how to convert HDExaminer files into the DynamX cluster format

Example Outputs

These are examples of files generated from Deuteros when following one of the tutorials. It includes:

• .pml and .py files which are used for visualisation in PyMOL and Chimera molecular graphics programs
• HDExaminer_example_dynamx.csv - the converted HDExaminer file generated in Tutorial 6.
• _Table_XX.csv files which are data tables that can be exported from the Data Tables tab in Deuteros during analysis.

Example Plots

• .svg vector files which contain exported plots generated in Deuteros. Examples of the coverage and redundancy plots, as well as advanced Woods, Butterfly and Volcano plots are included.