BridgeDb-Matlab functions

Functions to use the BridgeDb webservice in Matlab. BridgeDb is a tool for identifier mapping.

Learn about BridgeDb at http://www.bridgedb.org/ and read about it in this paper:

Van Iersel, M.; Pico, A.; Kelder, T.; Gao, J.; Ho, I.; Hanspers, K.; Conklin, B.; Evelo, C. BMC Bioinformatics 2010, 11, 5, https://doi.org/10.1186/1471-2105-11-5

The DOI of this repository is 10.5281/zenodo.5550067.

License: AGPL-3

BridgeDb-Matlab Usage Instructions:

Please download Matlab first, as well as Python (instructions). For Python, check if you use a supported version (version 2.7, 3.7, and 3.8 are currently supported) On the command line (Bash/Unix users):

python -V

Check if Python is setup correctly in Matlab, from the Matlab Command Window:

pe = pyenv

Download this repository:

git clone https://github.com/bridgedb/BridgeDb-matlab.git

Local Matlab installation:

• Start your version of Matlab [tested with Matlab 2021A]
• Add the folder where you downloaded this code (e.g. BridgeDb-matlab) to your working directory: Right-click, 'Add to Path'/'Selected Folders and Subfolders'

• Open the folder (double click or rightclick/Open). Your Current folder in Matlab should look like this now:

Matlab Online:

• Visit the matlab online page
• Upload the folder where you donwloaded this code (e.g. BridgeDb-matlab) to your Matlab Drive.

When the upload succeeded, you should see the BridgeDb-Matlab folde rin your drive, and in you Matlab Online Instance:

• Add the folder to your working directory:

Executing BridgeDb Code

• In the Matlab command window, type the following command to check your pathway directory:

pwd

• Switch to the folder containing your code (if needed):

cd('PATH/TO/FILE')

• Execute the XrefsBatch mapping function on the test data, located in the 'testData' folder, as such:

 xrefsBatch('BridgeDb-matlab/testData/case1-example.tsv', 'Homo sapiens', 'H')

• Your results are stored in your working directory, as a file called 'mappings.csv' (located in the folder testData):

• You can view your results by double clicking the mappings.csv file in the Matlab working directory: