CD2H gitForager

Sage Bionetworks

Login: Sage-Bionetworks

Company: null

Location: Seattle, Washington

email: null

Blog: www.sagebase.org

Members

Repositories

20150518_LINCS: Presentation for May 18, 2015 at OHSU for MEP-LINCS
20151027_U4C: Presentation for U4C
admincentral-infra: Infrastructure for the AWS AdminCentral account
ALSStratificiationChallenge: This is the project for the scoring process for the DREAM ALS Stratification Challenge
AMPAD_Data_Explorer: Shiny app for AMP-AD heatmap
ampad-DiffExp: Code base for performing covariate adjustments and differential expression analysis of the RNAseq data from AMP-AD.
AMP-AD_Driver_Prediction_Engine: null
AMPAD_Lineage: Ordering patients on smooth manifolds using lineage estimation tools
AMP-AD_Network_Analysis: location of analysis scripts for AMP-AD network working group
ampAdScripts: Scripts to migrate data from internal partner sites to public web-site
amp-rnaseq: Code for reprocessing the RNAseq data from AMP-AD.
AnalyticClientBuild: This repository contains the configuration for the build system for the Synapse analytic clients.
annotationUI: Annotation manifest generator
annotator: A Synapse annotations automation tool.
AppCore: Core code shared by the initial ResearchKit apps.
audit: Scripts for audit
audit-pipeline: null
aws-cf-templates: CloudFormation templates for AWS
aws-infra: Global Sage Bionetworks AWS Infrastructure
awsUbuntuSetup: bootstrap scripts for launching an ubuntu aws ec2 instance
aws-utilities: Utilities for Amazon Web Services (AWS)
BaylorSage: null
BCC: Sage/DREAM Breast Cancer Challenge R Package
bfrm: Bayesian Factor Regression Model (BFRM) techniques from West group at Duke - wrappers written to integrate as an R package to call platform-specific executable.
bfrmDemo: Demonstration code
bfrmSidebySide: Testing the R package against the native binary
bfrmTest: null
bootswatch: Themes for Bootstrap
Bridge: This package is defunct. Please use https://github.com/Sage-Bionetworks/BridgePF/ instead.
BridgeActivityNotificationWorker: null
BridgeAdminUI: An Admin App used by Bridge Dev Team to manage Bridge Study
BridgeAndroidSDK: null
BridgeApp-Apple-SDK: Shared code for developing ResearchSuite applications using Bridge services.
BridgeAppSDK: SDK for creating ResearchKit-based Bridge apps for iOS
bridge-base: Code shared by other Bridge packages
bridge-cookbooks: null
BridgeDataUploadUtils: Bridge Upload Utils for Archive and Encryption
BridgeDJengScripts: Making my own Scripts repository, since that's much easier than trying to integrate BridgeScripts
BridgeDocs: Bridge developer portal
Bridge-Exporter: Worker app to aggregate Bridge uploads, survey answers, and health data daily, and export them to Synapse
Bridge-Exporter-infra: Setup Bridge exporter infrastructure
BridgeExporterIntegrationTests: Integration test for Bridge Exporter
Bridge-EX-Scheduler: Bridge EX 2.0 Scheduler
Bridge-FitBit-Scheduler: null
Bridge-FitBit-Worker: Bridge Worker for FitBit Integration
Bridge-infra: Setup and configure Infrastructure for Bridge on AWS
BridgeIntegrationTests: Integration Tests for Bridge server
BridgeIntegTestUtils: null
Bridge-iOS-SDK: null
BridgeJavaSDK: Java SDK for the BridgePF server
BridgeJS: Bridge web client in JavaScript
BridgeMasterScheduler: null
BridgePF: Server software for Bridge-based mobile applications
BridgePF-infra: Infrastructure for BridgePF
bridgepf-utils: null
Bridge-Reporter: null
Bridge-Reporter-Scheduler: null
BridgeResearcherUI: Study management application for Bridge researchers
bridge-services: null
BridgeStaticPDandBCS: Marketing web sites for mPower and Share The Journey apps
BridgeStaticPD-NL: mPower application web site (Dutch language version)
BridgeTestUtils: shared test classes for Bridge Server
BridgeUserDataDownloadService: Bridge User Data Download (BUDD) Service
bridge-utils: null
BridgeWorkerIntegrationTests: null
BridgeWorkerPlatform: General platform holding all services in Bridge
BridgeWorkerPlatform-infra: Setup and configure Infrastructure for Bridge Worker Platform app on AWS
bridge-workers: null
bucket-antivirus-function: Serverless antivirus for cloud storage.
Cancer-Pathway-Sparse-Factor-Models: Industrial strength decomposition of signaling pathway perturbations in cancer...
CardiorespiratoryFitness-Android: null
CardiorespiratoryFitness-iOS: Stand-alone task modules for measuring cardiorespiratory fitness
CellTypeDeconv: Simulator for cell type deconvolution
CelltypeDeconvolution: Repository to host codes to estimate member cell type abundances from cell population, using gene expression data.
cfncluster-cookbook: The Chef cookbook used to build and bootstrap CfnCluster
challenge-bootstrap: Scripts for getting started with a Challenge
CI-Build-Tools: Collection of Gists
clearScience-demo: Code stored for the mocked up version of clearScience -- a real analysis with actual objects stored in Synapse
clearScience-Mark2-Demo: null
climbr: Access mouse metadata from the CLIMB API
CMSclassifier: null
CMSSupport: Drop-in Bridge-compatible CMS encryption implementation for use with AppCore.
cnvkit_cwl: null
CommonCompute: Common compute resources for Sage data scientists
common-utilities: Common utilities with zero dependencies.
CommunityDataReleases: Data release standard operating procedures for Sage Bionetworks communities
copy-thread-to-issue: Copies Synapse Discussion Forum threads to Github issues
crc-cms-kras: Study of the immunological impact of KRAS mutation and CMS subtype
CRC-RASness: null
crcsc: CRC Subtyping Consortium
CRFValidationApp: Application for validating CRF mobile health modules for the iPhone.
CSBCminiDREAM: Challenge resources & instructional material for CSBC Summer Research Program
csv-utilities: Utilities related to reading from and writing to a csv file
ctdd: cancer target drug discovery network
DARPA_Challenge: null
dashboard: null
dashboard-core: To be shared by all the dashboard packages
dashboard-dw: null
dashboard-ui: null
database-semaphore: null
database-utils: null
DataHub_T1D: DataHub - A Collaborative Network in Type 1 Diabetes
dcc-survey: null
dccvalidator: Validate CNS Data and Metadata
dccvalidator-app: null
dermalNF: Code designed to annotate and process CTF-funded dermal NF samples. All available data and key analysis steps uploaded to http://www.synapse.org/dermalNF
DM-Challenge-Writeup-Copytool: null
dm-volume-check: Checks the volume mounts for the prepreprocessing/training phase of the Digital Mammography challenge
dockerParallelRemoveDirectory: deletes directory files in parallel for the DM challenge
DockerRNAseq: null
dockstore-tool-synapse-get: Dockerized Synapse Python client & CWL for Dockstore
DOSE: Code from the paper Simulation Studies as Designed Experiments
DREAM9_Broad_Challenge_Scoring: This is the scoring application for the DREAM 9 Broad Gene Essentiality Prediction Challenge.
DREAM_Alzheimers_Challenge_Scoring: Scoring code for the Alzheimer's challenge
DREAM_DM_starter_code: Some starter code for training/testing some basic CNN models given our data.
dreamtools: Code sharing related to DREAM challenges
DREAM-Utilities: null
DummyPF: null
DummyPF-infra: null
EvaluationMailSync: EvaluationMailSync
EvaluationStatistics: This application computes statistics on the evaluation queues in Synapse. See https://sagebionetworks.jira.com/browse/CHAL-16 for more info.
fastq_mixer: A tool that mixes fastq files to generate a new mixed fastq
fastq_mixing_workflow_cwl: null
Federation: Federation Evaluation after peer review
federationPLoSRevision: null
Ferte-et-al-Review: Code repository for a review of bioinformatic procedures related to clinical biomarker development
file-proxy: Proxy for file upload and download.
FluDyNeMo: Code for managing the data of FlyDyNemo
Genie: For analyzing data in www.synapse.org/genie
genomeBrowsers: null
ggplotwithyourdata: R Shiny app as an inteface to ggplot2
ggplotWithYourDataOLD: Get a Synapse Table and do some plotting.
github-issues-to-synapse-lambda: Write open Github issues to a Synapse table
GitSandbox: null
Glioblastoma-Exploration: Scouring the Glioblastoma (GBM) TCGA expression data for molecular signatures indicative of survival benefit
gwtbootstrap3: GWT wrapper for the Bootstrap front-end framework
gwtbootstrap3-extras: Extra (third party) components for GwtBootstrap3
GwtVisualizationWrappers: GWT wrappers for common js visualization libraries
hbgdki-bootstrap: Project management code for HBGDki
HBGDki_Hackathon: Code examples for the Lisbon 2016 HBGDki Hackathon
Hello-World: Sample Repo
heroku-buildpack-scala: Heroku buildpack: Scala
ICGCSynapseGlue: This code connects the approved user list from ICGC to the Synapse approved participants list in the ICGC Dream 8.5 Challenge.
ICGC-TCGA-DREAM-Mutation-Calling-challenge-tools: Tools for participants in the ICGC-TCGA DREAM Mutation Calling challenge
Infectious-Disease-Challenge: null
Interactome: null
ISMB-AKES-challenge: null
jmeter_ncbo: Test performance of self-hosted Annotator service vs. NCBO-hosted Annotator service
js-host-test: null
JSON-java: A reference implementation of a JSON package in Java.
kallisto_cwl: files for using kallisto with cwl
knit2synapse: Functionality to knit RMarkdown documents to Synapse wiki pages.
logcentral-infra: Synapse LogCentral Infrastructure
markdown-it-synapse-server: Node.js based markdown-it web service - designed to be used for server-side Synapse markdown processing.
mayoeQTL: null
MEP_Processing: Preprocessing and analysis code for MEP-LINCS data
MEP_Processing: Preprocessing and analysis code for MEP-LINCS data
MEP_Processing: Preprocessing and analysis code for MEP-LINCS data
MEP_Processing: Preprocessing and analysis code for MEP-LINCS data
metadata-schema: This repo is for the metadata schemas associated with the HCA
metanetwork: metanetwork
metanetworkSynapse: null
mGenomics: null
mHealthTools: null
mhealthx: mhealthx is a software pipeline that automates feature extraction from mobile health data saved as a Synapse project (synapse.org).
minidream-challenge-2018: null
minidream-r-env: Resources for setting up and managing an RStudio environment for interactive mini-DREAM activities
misc_cwl: null
mogenerator: Core Data code generation
MoleMapper: null
moleMapperCuration: null
Mole-Mapper-Mover: This is a periodic job to copy v1 archived MoleMapper data to the live v2 MoleMapper tables for those patients who have consented to v2.
MoleMapper-sdata: scripts associated with the submission to Nature Scientific Data
mPower: ResearchKit app studying Parkinson disease, developed by Sage Bionetworks.
mPower-2-Android: Source code for the Android version of the mPower 2 study app.
mPower-2-iOS: Source code for the iOS version of the mPower 2 study app.
mpower-admin: The on boarding admin panel for AHPD
mPower-Android: mPower for Android
mPowerProcessing: null
mPower-sdata: scripts used for preparation of Nature Scientific Data submission and release of mPower data
mPowerSDK: Shared framework for ResearchKit app studying Parkinson's disease, developed by Sage Bionetworks and University of Rochester.
mPowerStatistics: An R package for the statistics used in mPower data processing
mpowertools: feature extraction toolkit for mPower modules
mPowerViz: Visualization view for mPower
Multiple-Myeloma-Challenge-Docker-Examples: Example Dockerized prediction models for the Multiple Myeloma DREAM Challenge
Multiple-Myeloma-Challenge-Examples: null
nbconvert-webapp: Converts ipynb file into html. Packaged for Lambda deployment
nbviewer: Nbconvert as a webservice (rendering ipynb to static HTML)
NCI-CPTAC-Challenge: null
NCI-CPTAC-Challenge-Examples: null
nda_aws_token_generator: Repository with sample code and libraries for obtaining AWS credentials to use with your NIMH Data Archives account
nfResources: Code to organize NF resources
NRGRSynapseGlue: This is the integration of NRGR and Synapse, linking data access approval in NRGR to data access in Synapse.
NTAP: This repository contains various analyses performed for the Neurofibromatosis Therapeutics Acceleration Program (NTAP).
nvml-cloudwatch: This utility collects GPU metrics from NVML and sends them to CloudWatch
nvml-statsd: This Python project integrates the NVIDIA management library with statsd to report GPU metrics to a monitoring tool
OlfactionDREAMChallenge: This is the software used to score the DREAM/Sage Olfaction Prediction Challenge
organizations-infra: Sage AWS Organizations
pancan-irwg-work: Analysis code for projects in the TCGA PanCancer Immune Response Working Groupo
PCBC_AMI: Packer build scripts for the AMI used at PCBC Stanford 2015 Training
pcbc_c4_analysis: Analysis of C4 data
PCBC_CardiacDiff_ShinyApp: A Shiny app to interact with PCBC CardiacDiff Data
PCBCDataExplorer: Interactive DataVis for PCBC expression data
PCBCDataTable: null
PCBC_ISATab: Generating PBC ISA-Tab files
PCBCLaboratoryPages: null
PCBCMonitor: Code that is run by Synapse user PCBCMonitor.
PCBCNetworkExplorer: null
pcbc-scidata: scripts used for preparation of Nature Scientific Data submission for the Progenitor Cell Biology Consortium
pcbcStats: Stats functions for PCBC analysis
PCBCUsageStatistics: null
PCC-Toolkit: Participant-Centered Consent (PCC) Toolkit - exploring a visual approach to assisting the ?informedness? part of informed consent for clinical studies.
PDBiomarkerChallenge: null
PDScores: null
PECShinyFacetedSearch: null
personalized_hypothesis_tests: Chaibub Neto et al. (2015) Personalized hypothesis tests for detecting medication response in Parkinson disease patients using iPhone sensor data.
pnfCellLines: This repository focuses on the NTAP-funded analysis regarding plexiform neurofibroma cell lines.
polypharmacology-db: This app enables exploration of the Drug-Target Explorer database.
predictiveModeling: null
PredictiveModel_pipeline: PredictiveModel_pipeline
PSON: Physical Sciences Oncology Network
PsychENCODE: null
PythonEmbedInR: Based off of PythonInR (https://bitbucket.org/Floooo/pythoninr/) but includes a standalone, compiled from source python instead of relying on the python installed on the host machine
pythonSynapseUtils: Helper Scripts to ease routine synapse python client oriented tasks
QuizEditor: Utility web app for editing Synapse Quiz JSON
QuizTextToJSONConverter: Utility for converting quiz text to JSON file suitable for reading by Synapse
rallyengine: R package driving parsing and production of rally inputs and outputs
ran: null
RCSLabs: Exploring tools and resources for reproducible computational science
Re-Attractor-Metagenes: Re-create Attractor Metagenes from PLoS Computation Biology Paper (Cheng et al)
redcapdd: Create REDCap data dictionaries
repo-scripts: Various scripts on the backend repository service
ResearchKit: ResearchKit is an open source software framework that makes it easy to create apps for medical research or for other research projects.
ResearchKitTranslator: A translation layer for using a ResearchKit task with ResearchSuite.
ResearchStackSampleApp: ResearchStack Sample App
SageResearch-Android: null
SageResearch-Android: null
ResearchSuite-AppleOS: Sage Research SDK is an open source software framework for modeling shared classes for use in research projects.
ResearchUXFactory-iOS: Factory methods for creating ResearchKit custom classes and steps
rGithubClient: Making it easier for R to talk to github
rHDF5: Access HDF5 files from R. Based on a package originally authored by Roy Kuraisa, Wilson Lau and Jason Eglin at Merck & Co. that was donated to Sage Bionetworks.
rnaseqSim: null
RNCryptor: CCCryptor (AES encryption) wrappers for iOS and Mac in Swift. -- For ObjC, see RNCryptor/RNCryptor-objc
rSCR: Sage Commons Repository
Rsftp: R package for sftp and other ssh-related functionality
rstudio: RStudio is an integrated development environment (IDE) for R
rSynapseClient: The R programmatic interface to Synapse services
rSynapseClientRewrite: The design of the R Synapse client is getting crusty and difficult to maintain. Let's overhaul it!
rSynapseUtilities: Utilities for use with the R Synapse Client
rWithPython: Package allowing R to call embedded/private copy of Python
SageBionetworksCoex: Compute gene coexpression based on gene expression data.
sageit-infra: Sage Bionetworks IT AWS infrastructure
SageLabMath: null
SageResearch: null
SageResearch-Android: null
SageResearch-Android: null
sandbox: null
sandbox-infra: Infra for sandbox application
sandboxpub: null
schema-to-pojo: The schema-to-pojo project was started because we wanted to programmatically generate the Plain Old Java Objects (POJOs) from JSON schemas. More specifically we wanted to use the generated POJOs as resources of the Synapse JSON REST web services API. Since we are using the POJOs as REST resources we also wanted an easy way to marsh instances to/from JSON. Lastly, we also wanted to use the generated POJOs in our Google Web Toolkit (GWT) client-side code and server side code. Thus the schema-to-pojo project was born. Learn more at the folllowing wiki:
scicomp-infra: null
seqtools: null
service-redirect: Simple services for redirecting from one host to another.
sessionTools: Store, load and teleport R sessions.
ShareTheJourney: ResearchKit app studying Breast Cancer, developed by Sage Bionetworks.
shinyModules: independent shiny modules for plug n play between applications
SimpleHttpClient: null
single-cell-seq: For all things related to single cell sequencing
Smart4SURE: null
SMC-DNA-Meta: null
SMC-Het-Challenge: Development of the automated scoring system for the SMC-Het Challenge
SMC-Het-Challenge-Examples: Galaxy tool integration examples for the SMC Het Challenge
SMC-RNA-Challenge: null
SMC-RNA-Examples: null
snm: Supervised Normalization of Microarrays (snm)
somatic-mutation-features: For aggregating seq-based features on somatic mutations and comparing them to features of input datasets.
sss: Shotgun Stochastic Search (SSS) from Hans, Dobra and West (http://pubs.amstat.org/doi/abs/10.1198/016214507000000121) - wrappers written to integrate as an R package to call platform-specific executable.
staging-ran: null
STM_clearScience: Source code for creating figures in STM paper
STM-metaAnalysis-clearScience: null
synAnnotationUtils: null
SynapseACLUpdate: ACL Update to fulfill PLFM-4258
synapse-admin: An administration client for Synapse
synapseAnnotations: Sage Bionetworks derived standards for annotating content in Synapse.
Synapse-Audit: null
synapsebridgehelpers: null
SynapseChallengeTemplates: A collection of templates for use by those writing Synapse challenge scoring applications. The aim is to provide executable examples in various languages (Python, R, Java).
synapse-demo: Synapse (www.synapse.org) demo script and supporting functions
synapsedev-infra: Synapse Development Infrastructure
synapseDocs: Synapse documentation pages
synapsedw-infra: Synapse Data Warehouse Infrastructure
synapsegraphdb: null
Synapse-Infra: Synapse infrastructure
Synapse-Markdown: Synapse Markdown Processor code
Synapse-Migration-Utility: Utility to migrate one Synapse stack to another
synapseMonitor: Command line tool for monitoring changes in a Synapse project
Synapse-Monitor: Simple Web Application for monitoring objects in Synapse
synapse-orchestrator: Synapse-based orchestrator for GA4GH workflows
synapseprod-infra: Synapse Production Infrastructure
synapseProjectUsageStatistics: null
synapsePythonClient: Programmatic interface to Synapse services for Python
synapse_python_client_cwl: null
synapser: An R package providing programmatic access to Synapse
synapseRAUtils: Create a useful and collaborative space for Research Associate's (RA) repetitive and overlapping tasks.
Synapse-React-Client: To help quickly integrate your React app with the Synapse API backend
Synapse-Repository-Services: The Synapse Repository Services project is the home of the JSON REST web services for Synapse.
synapserutils: R package for Synapse utilities
synapse-seq: Code for running/loading seq datasets using Synapse.
Synapse-Sftp-Proxy: null
SynapseShinyApp: Basic structure of a R Shiny application for use on Synapse
SynapseShinyFacetedSearch: null
SynapseSmokeTest: Smoke test for Synapse deployment
Synapse-Stack-Builder: Project for building a complete Synapse Stack
synapseTutorials: Small Vignettes of Synapse use
Synapse-User-Geolocation: An application to geolocate all Synapse users and display them on a map.
Synapse-Warehouse-Workers: Workers that maintain analytical data related to Synapse.
SynapseWebClient: The web client of the Synapse REST service core
synapsewiki: Create Synapse Wiki page from R Markdown
synapsify-demo: Source for demo analyses for Synapsify
synapsify-tests: testing functionality
syndccutils: code for managing data coordinating operations through Synapse
Synodos_NF2: null
Synodos_NF2_SyDE_shinyApp: Synodos Data Explorer(SyDE) Shiny App
SynSeq: Sequencing wrappers
TableTrigger: A Java project to monitor tables for changes and spawn Docker-based algorithms to process new content
tcgaImport: null
tcga-perturbations: Standardized perturbation signatures across TCGA
TeamStudyViz: Weekly survey report for TeamStudy
Tesla: null
to-be-removed-ran: Sage Bionetworks R Archive Network
Tumor-Deconvolution-Challenge: null
U4CChallenge: null
url-signer: A simple Java Utility for Signing URLs
vcf2maf: Convert VCF (Variant Call Format) into TCGA MAF (Mutation Annotation Format)
vdsDrugSensitivityShiny: Drug sensitivity shiny application
WallOfTargets: null
WallOfTargets: null
WallOfTargets: null
WallOfTargets: null
web-elevate-ms: elevateMS website
web-journey-pro: Journey PRO website
web-mpower-2: mPower 2.0 Enrollment Site
worker-utilities: null
workflow: null

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.