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https://github.com/Sage-Bionetworks/awesome-synapse

List of repositories here that utilizes the Synapse clients
https://github.com/Sage-Bionetworks/awesome-synapse

List: awesome-synapse

Last synced: 3 months ago
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List of repositories here that utilizes the Synapse clients

Host: GitHub
URL: https://github.com/Sage-Bionetworks/awesome-synapse
Owner: Sage-Bionetworks
License: apache-2.0
Created: 2021-01-22T04:34:21.000Z (almost 4 years ago)
Default Branch: main
Last Pushed: 2021-04-12T07:57:13.000Z (over 3 years ago)
Last Synced: 2024-08-09T19:24:50.515Z (3 months ago)
Size: 20.5 KB
Stars: 3
Watchers: 6
Forks: 1
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

ultimate-awesome - awesome-synapse - List of repositories here that utilizes the Synapse clients. (Other Lists / PowerShell Lists)

README

        # Awesome Synapse

A curated list of packages and tools using Synapse R, Python, React clients inspired by other awesome-* lists.

- [Portals](#portals)

- [R](#r)

  * [Shiny](#shiny)

- [Python](#python)

- [Java](#java)

- [Workflow](#workflow)

- [Lists](#lists)

- [Organizations](#rganizations)

## Portals

* [portals](https://github.com/Sage-Bionetworks/portals) - React component based configurations that generate community portals built on top of Synapse

* [Collaboration Portal](https://github.com/Sage-Bionetworks/sagebio-collaboration-portal) - Prototype Collaboration Portal

* [Agora](https://github.com/Sage-Bionetworks/Agora)

## R

* [syndccutils](https://github.com/Sage-Bionetworks/syndccutils) - Code for managing data coordinating operations (e.g., development of the CSBC/PS-ON Knowledge Portal and individual Center pages) for Sage-supported communities through Synapse.

* [synapseAnnotations](https://github.com/Sage-Bionetworks/synapseAnnotations/) - Sage Bionetworks derived standards for annotating content in Synapse. This provide a mechanism for defining, managing, and implementing controlled vocabularies when annotating content in Synapse.

* [sagethemes](https://github.com/Sage-Bionetworks/sagethemes) - The sagethemes package provides plot color palettes and themes that use the Sage Bionetworks branded colors.

* [challengerutils](https://github.com/Sage-Bionetworks/challengerutils) - The R version of `challengeutils`

* [dccmonitor](https://github.com/Sage-Bionetworks/dccmonitor) - This package is intended to assist Sage Bionetworks data curators to check the status of metadata and documentation files uploaded via the dccvalidator shiny application

* [mhealthtools](https://github.com/Sage-Bionetworks/mhealthtools) - A modular R package for extracting features from mobile sensor data

* [synapseforms](https://github.com/Sage-Bionetworks/synapseforms) - Wrappers for the [Synapse Forms Services API](https://docs.synapse.org/rest/#org.sagebionetworks.repo.web.controller.FormController).

* [knit2synapse](https://github.com/Sage-Bionetworks/knit2synapse) - Knit Rmarkdown files to Synapse wikis

### Shiny

* [SynapseShinyApp](https://github.com/Sage-Bionetworks/SynapseShinyApp) - Basic Shiny application for use on Sage Bionetwork's Synapse web portal.

* [data curator app](https://github.com/Sage-Bionetworks/data_curator) - Shiny application to annotate and ingest metadata (manifest) files

* [dccvalidator](https://sage-bionetworks.github.io/dccvalidator/index.html) - package and Shiny app to perform data validation and QA/QC

* [projectLive](https://github.com/Sage-Bionetworks/projectLive) - Track the impact of our funding partners in real time

* [Synodos_NF2](https://github.com/Sage-Bionetworks/Synodos_NF2_SyDE_shinyApp) - Synodos Data Explorer(SyDE) Shiny App

* [PCBC](https://github.com/Sage-Bionetworks/PCBCDataExplorer) - PCBC Shiny Application

* [shinyModules](https://github.com/Sage-Bionetworks/shinyModules) - independent shiny modules for plug n play between applications

## Python

* [s3-synapse-sync](https://github.com/Sage-Bionetworks/s3-synapse-sync) - Lambda function code to index files in S3 buckets by creating filehandles on Synapse, triggered by file changes to S3.

* [schematic](https://github.com/Sage-Bionetworks/schematic) - Python package for Biomedical Data model and Data Ingress Management

* [challengeutils](https://github.com/Sage-Bionetworks/challengeutils/pull/204/files) - Synapse challenge utility functions + more

* [synapseformation](https://github.com/Sage-Bionetworks/synapseformation) - Client for using [Synapse Formation templates](https://github.com/Sage-Bionetworks/synapse-formation-templates).

* [synapseMonitor](https://github.com/Sage-Bionetworks/synapseMonitor) - Monitor a Synapse Project / entities scoped by a Synapse file view.

* [synapsegenie](https://github.com/Sage-Bionetworks/synapsegenie) - Crawl through Synapse files to validate and process them given a plugin file format registry.

* [prov-service](https://github.com/Sage-Bionetworks/prov-service) - lightweight implementation of the Synapse Activity services, based on the PROV spec

## Java

* [SynapseWorkflowOrchestrator](https://github.com/Sage-Bionetworks/SynapseWorkflowOrchestrator) - Links one or more Synapse Evaluation queues to a workflow engine. Each Evaluation queue is associated with a workflow template. Each submission is a workflow job, an instance of the workflow template. Upon submission to the Evaluation queue the Workflow Orchestrator initiates and tracks the workflow job, sending progress notifications and uploading log files.

* [NRGRSynapseGlue](https://github.com/Sage-Bionetworks/NRGRSynapseGlue) - This is the integration of NRGR and Synapse, linking data access approval in NRGR to data access in Synapse.

* [EvaluationStatistics](https://github.com/Sage-Bionetworks/EvaluationStatistics) - This application computes statistics on the evaluation queues in Synapse.

* [Synapse-User-Geolocation](https://github.com/Sage-Bionetworks/Synapse-User-Geolocation) - An application to geolocate all Synapse users and display them on a map.

## Workflow

* [CWL Synapse Client](https://github.com/Sage-Bionetworks-Workflows/dockstore-tool-synapseclient) - CWL interface to Synapse command line.

* [nextflow Synapse Client](https://github.com/Sage-Bionetworks/synapse-nextflow) - Nextflow interface to Synapse command line.

* [rare-disease-workflows](https://github.com/Sage-Bionetworks/rare-disease-workflows) - Workflows for processing rare disease data on Synapse.

## Lists

* [Data Coordination Tools](https://github.com/Sage-Bionetworks/data-coordination-tools) - This repository gathers existing tools used for data coordination at Sage.

## Organizations

* [Sage-Bionetworks-Workflows](https://github.com/Sage-Bionetworks-Workflows) - List of dockstore tools and workflows.

* [Sage-Bionetworks-Challenges](https://github.com/Sage-Bionetworks-Challenges) - Sage Bionetworks hosts crowdsourcing challenges that examine questions in biology and medicine.