README.md
In Sage-Bionetworks/agoradataprocessing: Process Data from Synapse for AMP-AD Agora
⚠️ DEPRECATED REPOSITORY
This repository has been deprecated and is no longer maintained.
- No further development will occur in this repository.
- This repository will not be monitored.
New Repository Location
Agora's data processing is now managed via the agora-data-tools project:
https://github.com/Sage-Bionetworks/agora-data-tools
For information, see the agora-data-tools README).
Agora Data Processing
R package and command line utility for processing data from Synapse to Agora. This required permissions to read and write to specific location in Synapse. Data is stored in the Synapse project at https://www.synapse.org/agora.
To process all Agora data from Synapse files to JSON files suitable for import into the Agora MongoDB, use (exec/process.R), which requires the config.json file. Providing the --store parameter will store the results to Synapse.
exec/./process.R --config config.json --store
If changes to the gene database used are needed, run inst/getMyGeneInfo.R to get gene information from mygene.info. This puts the resulting data into Synapse. This step is required to run separately due to conflicts between the synapser and mygene R packages.
The output of this tool is used by the Agora data manager.
Development
Create a feature branch from master for doing development. You can test the data processing locally using the exec/process.R command mentioned above. Note that there are separate configurations for staging and production. You will manually run the processing command when your code is ready, as CICD is not set up in this repository (yet).
Releases
Use semantic versioning for releases.
Sage-Bionetworks/agoradataprocessing documentation built on June 14, 2025, 11:08 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
⚠️ DEPRECATED REPOSITORY
This repository has been deprecated and is no longer maintained. - No further development will occur in this repository. - This repository will not be monitored.
New Repository Location
Agora's data processing is now managed via the agora-data-tools project:
https://github.com/Sage-Bionetworks/agora-data-tools
For information, see the agora-data-tools README).
Agora Data Processing
R package and command line utility for processing data from Synapse to Agora. This required permissions to read and write to specific location in Synapse. Data is stored in the Synapse project at https://www.synapse.org/agora.
To process all Agora data from Synapse files to JSON files suitable for import into the Agora MongoDB, use (exec/process.R), which requires the config.json file. Providing the --store parameter will store the results to Synapse.
exec/./process.R --config config.json --store
If changes to the gene database used are needed, run inst/getMyGeneInfo.R to get gene information from mygene.info. This puts the resulting data into Synapse. This step is required to run separately due to conflicts between the synapser and mygene R packages.
The output of this tool is used by the Agora data manager.
Development
Create a feature branch from master for doing development. You can test the data processing locally using the exec/process.R command mentioned above. Note that there are separate configurations for staging and production. You will manually run the processing command when your code is ready, as CICD is not set up in this repository (yet).
Releases
Use semantic versioning for releases.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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