ctuning-programsCollective Knowledge extension with unified and customizable benchmarks (with extensible JSON meta information) to be easily integrated with customizable and portable Collective Knowledge workflows. You can easily compile and run these benchmarks using different compilers, environments, hardware and OS (Linux, MacOS, Windows, Android). More info:
Stars: ✭ 41 (-52.33%)
ipython2cwlIPython2CWL is a tool for converting IPython Jupyter Notebooks to CWL Command Line Tools by simply providing typing annotation.
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janis[Alpha] Janis: an open source tool to machine generate type-safe CWL and WDL workflows
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DUNCode for "Depth Uncertainty in Neural Networks" (https://arxiv.org/abs/2006.08437)
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GGR-cwlCWL tools and workflows for GGR
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CD4-csawReproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
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awflowReproducible research and reusable acyclic workflows in Python. Execute code on HPC systems as if you executed them on your personal computer!
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tibannaTibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
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lumberjackTrack changes in data with ease
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microbiomeHDCross-disease comparison of case-control gut microbiome studies
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cwl-tsTypescript data model for Common Workflow Language
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ITKSphinxExamplesCookbook examples for the Insight Toolkit documented with Sphinx
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sunbeamA robust, extensible metagenomics pipeline
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Topcuoglu ML mBio 2020Best practices for applying machine learning to bacterial 16S rRNA gene sequencing data
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VIRTUSA bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
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reskitA library for creating and curating reproducible pipelines for scientific and industrial machine learning
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OAProgressionMultimodal Machine Learning-based Knee Osteoarthritis Progression Prediction from Plain Radiographs and Clinical Data
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GSoC-IdeasCloudCV GSoC 2021 Ideas
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wrenchWRENCH: Cyberinfrastructure Simulation Workbench
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nonparametric-bayes📓 Non-parametric Bayesian Inference for Conservation Decisions
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ck-crowd-scenariosPublic scenarios to crowdsource experiments (such as DNN crowd-benchmarking and crowd-tuning) using Collective Knowledge Framework across diverse mobile devices provided by volunteers. Results are continuously aggregated at the open repository of knowledge:
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openscienceEmpirical Software Engineering journal (EMSE) open science and reproducible research initiative
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researchcompendiumNOTE: This repo is archived. Please see https://github.com/benmarwick/rrtools for my current approach
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GeneTonicEnjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
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dxCompilerWDL and CWL compiler for the DNAnexus platform
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targets-minimalA minimal example data analysis project with the targets R package
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publicationsIMS Machine Learning Lab publications.
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crowdsource-experiments-using-android-devicesAndroid application to participate in experiment crowdsourcing (such as workload crowd-benchmarking and crowd-tuning) using Collective Knowledge Framework and open repositories of knowledge:
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eventsMaterials related to events I might attend, and to talks I am giving
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rmdTemplatesRmarkdown templates for reproducible science
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datascienceKeeping track of activities around research data
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dicyA builder for LaTeX, knitr, literate Agda, literate Haskell and Pweave that automatically builds dependencies.
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workflowsBioinformatics workflows developed for and used on the St. Jude Cloud project.
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emg-viral-pipelineVIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
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showyourworkFully reproducible, open source scientific articles in LaTeX.
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emp🔬 Empirical CLI
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us-rawdata-sdaA Deep Learning Approach to Ultrasound Image Recovery
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affiliate-marketing-disclosuresCode and data belonging to our CSCW 2018 paper: "Endorsements on Social Media: An Empirical Study of Affiliate Marketing Disclosures on YouTube and Pinterest".
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dockstoreOur VM/Docker sharing infrastructure and management component
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hotsubCommand line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources
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ngs-preprocessA pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
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scriptcwlCreate cwl workflows by writing a simple Python script
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ukbrestukbREST: efficient and streamlined data access for reproducible research of large biobanks
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wdl2cwl[Experimental] Workflow Definition Language (WDL) to CWL
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RepSePReproducible Self-Publishing - Demo Publications in the Most Common Formats
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genepattern-notebookPlatform for integrating genomic analysis with Jupyter Notebooks.
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idealInteractive Differential Expression AnaLysis - DE made accessible and reproducible
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DaCyDaCy: The State of the Art Danish NLP pipeline using SpaCy
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bentenA language server for Common Workflow Language
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ck-webCollective Knowledge web extension to browse CK repositories, visualize interactive graphs and articles, render CK-based websites, implement simple web services with JSON API (for example to crowdsource experiments or unify access to DNN). Demos of interactive articles, graphs and crowdsourced experiments:
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bacannotGeneric but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
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pytaskpytask is a workflow management system which facilitates reproducible data analyses.
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