https://github.com/bridgedb/bridgedb-matlab
Functions to use the BridgeDb webservice in Matlab. BridgeDb is a tool for identifier mapping.
Science Score: 31.0%
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✓CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 5 DOI reference(s) in README -
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Low similarity (12.3%) to scientific vocabulary
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Functions to use the BridgeDb webservice in Matlab. BridgeDb is a tool for identifier mapping.
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README.md
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:
Matlab
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:
Matlab pwd Switch to the folder containing your code (if needed):
Matlab cd('PATH/TO/FILE')Execute the XrefsBatch mapping function on the test data, located in the 'testData' folder, as such:
Matlab 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:
Owner
- Name: BridgeDb
- Login: bridgedb
- Kind: organization
- Location: Netherlands
- Website: https://www.bridgedb.org/
- Repositories: 37
- Profile: https://github.com/bridgedb
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: BridgeDb
version: 3.0.13
date-released: 2021-12-31
url: "https://github.com/bridgedb/BridgeDb"
preferred-citation:
- type: article
authors:
- family-names: Van Iersel
given-names: Martijn P.
- family-names: Pico
given-names: Alexander R.
- family-names: Kelder
given-names: Thomas
- family-names: Gao
given-names: Jianjiong
- family-names: Isaac
given-names: Ho
- family-names: Hanspers
given-names: Kristina
- family-names: Conklin
given-names: Bruce R.
- family-names: Evelo
given-names: Chris T.
title: "The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services"
year: 2010
journal: BMC Bioinformatics
volume: 11
issue: 5
doi: 10.1186/1471-2105-11-5
url: https://doi.org/10.1186/1471-2105-11-5