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Search results for reproducible research

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379 search results found

Targets Shiny ⭐ 60

Example Shiny app containing a targets pipeline.

Lumberjack ⭐ 59

Track changes in data with ease

Panoptes ⭐ 59

Monitor computational workflows in real time

Itkpythonpackage ⭐ 59

A setup script to generate ITK Python Wheels

Drake Examples ⭐ 58

Example workflows for the drake R package

Oaprogression ⭐ 58

Multimodal Machine Learning-based Knee Osteoarthritis Progression Prediction from Plain Radiographs and Clinical Data

The user manual for the drake R package

Chembl Downloader ⭐ 55

Write reproducible code for getting and processing ChEMBL

Nozzle is a report generation toolkit for data analysis pipelines implemented in R.

Benchpress ⭐ 52

A Snakemake workflow to run and benchmark structure learning (a.k.a. causal discovery) algorithms for probabilistic graphical models.

Code for "Depth Uncertainty in Neural Networks" (https://arxiv.org/abs/2006.08437)

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

Pcaexplorer ⭐ 51

pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data

Itksphinxexamples ⭐ 50

Cookbook examples for the Insight Toolkit documented with Sphinx

Biosimspace ⭐ 48

An interoperable Python framework for biomolecular simulation.

Variational Sparse Coding ⭐ 47

Reproducing the paper "Variational Sparse Coding" for the ICLR 2019 Reproducibility Challenge

moai is a PyTorch-based AI Model Development Kit (MDK) created to improve data-driven model workflows, design and reproducibility.

Open Solution Googleai Object Detection ⭐ 46

Open solution to the Google AI Object Detection Challenge 🍁

Ck Artifact Evaluation ⭐ 46

Collective Knowledge repository to support artifact evaluation and reproducibility initiatives:

Reprohack Hq ⭐ 46

ReproHack Headquarters

Ten Simple Rules Dockerfiles ⭐ 45

Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science

Targets Minimal ⭐ 45

A minimal example data analysis project with the targets R package

Research Software Directory ⭐ 44

The Research Software Directory is a content management system that is tailored to software.

Reproducible Research in Ecology, Evolution, Behaviour, and Environmental Studies

🔬 Empirical CLI

Open Science With R ⭐ 43

⛔️ [SUSPENDED] Writing the rOpenSci book on GitHub

Reproducible Audio Research ⭐ 43

List of Reproducible Audio Research Papers

creating optimal conditions for reproducibility

Analysispreservation.cern.ch ⭐ 42

Source code for the CERN Analysis Preservation portal

Genepattern Notebook ⭐ 41

Platform for integrating genomic analysis with Jupyter Notebooks.

Ctuning Programs ⭐ 41

Collective 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:

Dime Standards ⭐ 41

Repository with resources for DIME's research standards and coding standards

Reproducible ⭐ 40

A set of tools for R that enhance reproducibility beyond package management

Microbiomehd ⭐ 40

Cross-disease comparison of case-control gut microbiome studies

Testipynb ⭐ 39

unit-testing for a collection of jupyter notebooks using nbconvert

Openscope_databook ⭐ 39

OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈

Prodigenr ⭐ 36

Project directory generator R package

Rcompendium ⭐ 36

📦 Create a package or compendium structure

Noise Phenomena ⭐ 36

📓 Ecology Letters review paper: Noise-driven phenomena in population biology

Ck Analytics ⭐ 35

Collective Knowledge repository with actions to unify the access to different predictive analytics engines (scipy, R, DNN) from software, command line and web-services via CK JSON API:

Snakemake Econ R ⭐ 35

reproducible research project template for R using Renv and snakemake with an econ application

Network Performance Framework: easy-to-use experiment manager with automated testing, result collection, and graphing

Example Get Started Experiments ⭐ 33

Get started DVC project

Rep Res Course ⭐ 33

Materials for a class on reproducible research with R, Rstudio, and GitHub

Software Dev ⭐ 33

Coding Standards for the USC Biostats group

Repro is a library for easily running code from published papers via Docker.

APPIAN is an open-source automated software pipeline for analyzing PET images in conjunction with MRI. The goal of APPIAN is to make PET tracer kinetic data analysis easy for users with moderate computing skills and to facilitate reproducible research.

WRENCH: Cyberinfrastructure Simulation Workbench

Knitr_knutshell ⭐ 31

knitr in a nutshell: a brief guide to knitr

👜 Easily pick a place to store data for your Python code.

Mlrhyperopt ⭐ 31

Easy Hyper Parameter Optimization with mlr and mlrMBO.

Collective 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:

Reproducible Research

Experimental eNvironment for OpenStack 🐒

Ck Crowdtuning Platforms ⭐ 30

Meta information about platforms participating in experiment crowdsourcing using Collective Knowledge Framework (OS,CPU,GPU,GPGPU,NN...):

Ck Docker ⭐ 30

Collective Knowledge extension to automate Docker "build","run" and "push" functions and packge CK repositories for collaborative and reproducible research:

Daiquiri ⭐ 30

Data quality reporting for temporal datasets.

Polyaxon Quick Start ⭐ 29

A quick start project for polyaxon

Openscience ⭐ 29

Empirical Software Engineering journal (EMSE) open science and reproducible research initiative

Repro Case Studies ⭐ 29

Reproducibility case study contributions

Wfcommons ⭐ 28

WfCommons: A Framework for Enabling Scientific Workflow Research and Development

Scipy Tutorial 2014 ⭐ 28

Tutorial on reproducible research practices at SciPy 2014

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Drugbank_downloader ⭐ 27

Don't worry about DrugBank licensing - write code that knows how to download it automatically

Reproducibility 2014 ⭐ 27

Talk on reproducible research at SURF: http://www.meetup.com/R-Users-Sydney/events/199742

Vtkpythonpackage ⭐ 27

A setup script to generate VTK Python Wheels

Binderhub Deploy ⭐ 27

Deploy a BinderHub from scratch on Microsoft Azure

ukbREST: efficient and streamlined data access for reproducible research of large biobanks

An image analysis workflow for open and reproducible research on femoral knee cartilage

User2016 Tutorial Jupyter ⭐ 26

R for Reproducible Research tutorial

Dime Latex Templates ⭐ 26

DIME's LaTeX templates and LaTeX exercises teaching anyone new to LaTeX how to use LaTeX and how to use DIME's templates

A library for creating and curating reproducible pipelines for scientific and industrial machine learning

How To Read A Research Compendium ⭐ 26

"How to Read a Research Compendium" - based on S. Keshav's "How to Read a Paper"

Confidentlearning Reproduce ⭐ 26

Official data release to reproduce Confident Learning paper results

Reproducible_paper_template ⭐ 25

Template repository for starting a new empirical paper project implementing good practices for reproducibility using R

Make Example ⭐ 25

An example of using make for a data analysis project

BRAPH 2.0 is a comprehensive software package for the analysis and visualization of brain connectivity data, offering flexible customization, rich visualization capabilities, and a platform for collaboration in neuroscience research.

Reproduce Ck Paper ⭐ 24

Shared artifacts in the Collective Knowledge Format as a proof-of-concept to reproduce our recent Collective Mind- and Collective Knowledge-related papers

Researchcompendium ⭐ 24

NOTE: This repo is archived. Please see https://github.com/benmarwick/rrtools for my current approach

Projects ⭐ 24

Hash Grid Encoding ⭐ 24

Pure PyTorch implementation of Nvidia's hash grid encoding: https://nvlabs.github.io/instant-ngp/

Crowdsource Experiments Using Android Devices ⭐ 24

Android application to participate in experiment crowdsourcing (such as workload crowd-benchmarking and crowd-tuning) using Collective Knowledge Framework and open repositories of knowledge:

Ck Crowd Scenarios ⭐ 23

Public 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:

Rr Jupyter Hackathon Jan 2017 ⭐ 23

Curriculum Development Hackathon on Reproducible Research using Jupyter Notebooks, to be held Jan 9-11 at BIDS in Berkeley, CA

Us Rawdata Sda ⭐ 23

A Deep Learning Approach to Ultrasound Image Recovery

A toolbox for writing Sweave or other LaTeX-based papers and reports and to prettify the output of various estimated models.

Umls_downloader ⭐ 23

Don't worry about UMLS, RxNorm, SNOMED, or SemMedDB licensing - write code that knows how to download it automatically

Essential_skills_rrc ⭐ 23

Essential skills for reproducible research computing

Miscellaneous tools for reproducible research with R.

Ngs Preprocess ⭐ 23

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Windows version of StatTag

Learning_r ⭐ 22

List of resources for learning R

Reproducibilty Challenge Ecanet ⭐ 22

Unofficial Implementation of ECANets (CVPR 2020) for the Reproducibility Challenge 2020.

Docker containers for bioinformatics with a small footprint

A builder for LaTeX, knitr, literate Agda, literate Haskell and Pweave that automatically builds dependencies.

Openplantpathology ⭐ 20

Open Plant Pathology website

Reproducibility_in_plant_pathology ⭐ 20

A systematic/quantitative review of articles, which provides a basis for identifying what has been done so far in the field of plant pathology research reproducibility and suggestions for ways to improving it.

Manuscript ⭐ 19

This repository implements an automated system to write our collaborative manuscript, while tracking changes and contributions.

Mex Vocabulary ⭐ 19

MEX Vocabulary: a lightweight machine learning interchange format

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