GitHub topics: reproducible-research

Repositories

ratschlab/he2st

Code of the paper "DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images"

Language: Jupyter Notebook - Size: 121 MB - Last synced at: about 7 hours ago - Pushed at: about 8 hours ago - Stars: 6 - Forks: 1

ReproNim/reprostim

Automated capture of audio-visual stimuli into BIDS datasets

Language: Python - Size: 38.4 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 5 - Forks: 4

neuhausi/canvasxpress-js

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.

Language: CSS - Size: 39.3 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 8 - Forks: 0

genepattern/genepattern-server

The GenePattern Server web application

Language: HTML - Size: 950 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 36 - Forks: 18

neuhausi/canvasXpress

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.

Language: R - Size: 116 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 297 - Forks: 45

vanheeringen-lab/seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Language: Python - Size: 1.39 GB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 156 - Forks: 28

jatanRT/eprscope

R package to process and analyze data and spectra in Electron Paramagnetic Resonance spectroscopy for chemists

Language: R - Size: 58.6 MB - Last synced at: about 6 hours ago - Pushed at: about 7 hours ago - Stars: 0 - Forks: 0

federicomarini/GeneTonic

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Language: R - Size: 121 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 78 - Forks: 10

RePlasma/RePlasma.github.io

Reproduced papers in Plasma Physics and beyond

Language: HTML - Size: 1.36 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 6 - Forks: 0

robervz22/Optimal-Play-Pig

Replication and reproduction of the results in the article: Optimal Play of the Dice Game Pig by Neller and Presser 2004

Language: Python - Size: 71.3 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0

aaronpeikert/repro-workshop

Language: R - Size: 8.57 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 20 - Forks: 24

seaflow-uw/seaflow-sfl

SFL files contain metadata for each SeaFlow files recorded during the cruise. These metadata are provided by the ship's data broadcast system and are being copied to the SeaFlow instrument as is.

Language: HTML - Size: 51.6 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 2 - Forks: 2

worldbank/wb-reproducible-research-repository

This repository supports the World Bank's Reproducible Research Repository

Language: Stata - Size: 696 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 12 - Forks: 1

ReproducibiliTea-org/reproducibiliTea

Website for the ReproducibiliTea Journal Club and Podcast

Language: HTML - Size: 6.81 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 8 - Forks: 26

nextflow-io/nextflow

A DSL for data-driven computational pipelines

Language: Groovy - Size: 58.2 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 2,922 - Forks: 684

ropensci/rix

Reproducible Data Science environments for R with Nix

Language: R - Size: 14.6 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 249 - Forks: 17

rubenarslan/formr.org

Chain simple surveys into longer runs to build complex studies. Use R to generate pretty feedback and complex designs.

Language: PHP - Size: 96.4 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 141 - Forks: 37

CenterForOpenScience/community

This repository contains all community documentation for contributing to our open-source projects, including guidelines, workflows, and resources to help new and returning contributors collaborate effectively in support of open science and reproducible research.

Size: 69.3 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 5 - Forks: 2

InsightSoftwareConsortium/ITK

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

Language: C++ - Size: 213 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 1,495 - Forks: 691

calkit/calkit

A framework and toolkit for analytical/research projects, with an emphasis on reproducibility.

Language: Python - Size: 8.67 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 20 - Forks: 0

klb2/reproducible-paper-python-template

Template for Python code with focus on accompanying a paper in order to allow reproducing the results

Language: Python - Size: 96.7 KB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 0

pipefunc/pipefunc

Lightweight fast function pipeline (DAG) creation in pure Python for scientific workflows 🕸️🧪

Language: Python - Size: 2.11 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 357 - Forks: 14

IDSIA/sacred

Sacred is a tool to help you configure, organize, log and reproduce experiments developed at IDSIA.

Language: Python - Size: 5.87 MB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 4,297 - Forks: 382

RecSysEvaluation/SIGIR2022-2024-reproducibility-audit

“We share our code online: Why this is not enough to ensure reproducibility and progress in recommender systems research

Size: 1.89 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

ddsjoberg/gtsummary

Presentation-Ready Data Summary and Analytic Result Tables

Language: R - Size: 690 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1,109 - Forks: 133

NeurodataWithoutBorders/nwb_hackathons

Repository for collecting materials from nwb hackathons

Language: Jupyter Notebook - Size: 378 MB - Last synced at: about 23 hours ago - Pushed at: 1 day ago - Stars: 24 - Forks: 84

ReverendBayes/Telecom-Churn-Predictor

Predicts which telecom customers are likely to churn with 95% accuracy using real-world data features from usage, billing, and support data. Implements Sturges-based binning, one-hot encoding, stratified 80/20 train-test split, and a two-level ensemble pipeline with soft voting. Achieves 94.60% accuracy, 0.8968 AUC, 0.8675 precision, 0.7423 recall.

Language: Python - Size: 242 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0

ropensci/targets

Function-oriented Make-like declarative workflows for R

Language: R - Size: 6.91 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 994 - Forks: 75

ElNiak/PANTHER

This tool presents a novel approach to bolstering network protocol verification by integrating the Shadow network simulator with the Ivy formal verification tool to check time properties. Furthermore, it extends Ivy’s capabilities with a dedicated time module, enabling the verification of complex quantitative-time properties.

Language: C - Size: 1.2 GB - Last synced at: 2 days ago - Pushed at: 2 months ago - Stars: 38 - Forks: 3

ropensci/geotargets

Targets extensions for geospatial data

Language: R - Size: 3.65 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 80 - Forks: 5

FR-RN/FR-RN

French Reproducibility Network website

Language: SCSS - Size: 64.3 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 11 - Forks: 21

LAMDA-CL/PyCIL

PyCIL: A Python Toolbox for Class-Incremental Learning

Language: Python - Size: 2.6 MB - Last synced at: 4 days ago - Pushed at: 22 days ago - Stars: 923 - Forks: 143

comic/grand-challenge.org

A platform for end-to-end development of machine learning solutions in biomedical imaging

Language: Python - Size: 63.8 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 178 - Forks: 54

NA-MIC/ProjectWeek

Website for NA-MIC Project Weeks

Language: HTML - Size: 1.07 GB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 86 - Forks: 296

colinbrislawn/q2-forums

Colin's notes for Qiime2 forums questions

Language: HTML - Size: 3.27 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

Cloud-CV/EvalAI

:cloud: :rocket: :bar_chart: :chart_with_upwards_trend: Evaluating state of the art in AI

Language: Python - Size: 63.5 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1,845 - Forks: 862

DeepMIMO/DeepMIMO

DeepMIMO Toolchain: Bridging RayTracers and 5G/6G Simulators

Language: Python - Size: 36.4 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 2 - Forks: 0

CoLRev-Environment/search-query

Search Query: A Python package designed to load, lint, translate, save, improve, and automate academic literature search queries.

Language: Python - Size: 580 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 3 - Forks: 6

wfcommons/WfCommons

WfCommons: A Framework for Enabling Scientific Workflow Research and Development

Language: Python - Size: 178 MB - Last synced at: about 22 hours ago - Pushed at: 8 days ago - Stars: 33 - Forks: 13

ropensci/git2rdata

An R package for storing and retrieving data.frames in git repositories.

Language: R - Size: 2.89 MB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 101 - Forks: 13

rostools/r-cubed-intermediate

Reproducible Research in R: An Intermediate Workshop on Modern Approaches and Workflows to Processing Data

Language: TeX - Size: 28 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 5 - Forks: 4

ropensci/gittargets

Data version control for reproducible analysis pipelines in R with {targets}.

Language: R - Size: 1.5 MB - Last synced at: about 6 hours ago - Pushed at: 10 months ago - Stars: 88 - Forks: 1

iterative/example-get-started

Get started DVC project (NLP, random forest)

Language: Python - Size: 22.5 KB - Last synced at: 3 days ago - Pushed at: 12 months ago - Stars: 180 - Forks: 184

tbarbette/npf

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

Language: Python - Size: 4.19 MB - Last synced at: 5 days ago - Pushed at: 16 days ago - Stars: 43 - Forks: 16

federicomarini/ideal

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Language: R - Size: 26.3 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 29 - Forks: 7

federicomarini/pcaExplorer

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

Language: R - Size: 60 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 56 - Forks: 17

BrazilianReproducibilityInitiative/bri-analysis

Analysis code for the Brazilian Reproducibility Initiative.

Language: R - Size: 1.27 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 1 - Forks: 0

razvanazamfirei/prism-score

Stata PRISM Score Calculation

Language: Stata - Size: 724 MB - Last synced at: 4 days ago - Pushed at: 8 months ago - Stars: 2 - Forks: 0

luciorq/condathis

Run any CLI tool on a Reproducible Isolated Environment ⚙️⚡

Language: R - Size: 777 KB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 10 - Forks: 1

InsightSoftwareConsortium/itkwidgets

An elegant Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.

Language: Python - Size: 76.9 MB - Last synced at: 7 days ago - Pushed at: about 2 months ago - Stars: 600 - Forks: 83

AntixK/PyTorch-VAE

A Collection of Variational Autoencoders (VAE) in PyTorch.

Language: Python - Size: 45.4 MB - Last synced at: 9 days ago - Pushed at: about 2 months ago - Stars: 7,111 - Forks: 1,123

LilValero/Human-Exome-Variant-calling-Using-Illumina-Data

Bioinformatics pipeline for Illumina human exome variant calling using FastQC, Trimmomatic, BWA, Samtools, Bcftools, and SnpEff. Demonstrates a reproducible workflow for NGS data analysis. #bioinformatics #genomics #variant-calling #ngs #pipeline

Language: HTML - Size: 0 Bytes - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 0 - Forks: 0

StatTag/StatWrap

StatWrap

Language: JavaScript - Size: 7.12 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 4 - Forks: 19

InsightSoftwareConsortium/InsightJournal

Insight Journal

Language: JavaScript - Size: 18.6 MB - Last synced at: 2 days ago - Pushed at: 10 days ago - Stars: 10 - Forks: 5

leipzig/awesome-reproducible-research

A curated list of reproducible research case studies, projects, tutorials, and media

Language: Python - Size: 1.42 MB - Last synced at: 4 days ago - Pushed at: 15 days ago - Stars: 343 - Forks: 39

nf-core/references

nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

Language: Nextflow - Size: 868 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 14 - Forks: 5

lre-security-systems-team/gpml

Language: HTML - Size: 5.38 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 4 - Forks: 0

NVlabs/sionna

Sionna: An Open-Source Library for Research on Communication Systems

Language: Jupyter Notebook - Size: 254 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 987 - Forks: 283

insightsengineering/crane

Supplement to functions found in the {gtsummary} R package

Language: R - Size: 4.17 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 4 - Forks: 0

edquant/edh7916

Course materials and website for EDH7916: Contemporary Research in Higher Education

Language: HTML - Size: 103 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 3 - Forks: 1

dpiotrkowski/notatki_PSI

Notatki z zajęć z Projektowania systemów informatycznych

Language: HTML - Size: 6.93 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 1 - Forks: 0

braph-software/BRAPH-2

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.

Language: MATLAB - Size: 1.12 GB - Last synced at: 9 days ago - Pushed at: 11 days ago - Stars: 47 - Forks: 13

showyourwork/showyourwork

A workflow for reproducible and open scientific articles

Language: TeX - Size: 13.7 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 600 - Forks: 49

JunoLab/Weave.jl

Scientific reports/literate programming for Julia

Language: Julia - Size: 10.3 MB - Last synced at: 8 days ago - Pushed at: 9 months ago - Stars: 842 - Forks: 94

felixleopoldo/benchpress

Scalable open-source software to run, develop, and benchmark causal discovery algorithms

Language: Python - Size: 123 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 68 - Forks: 17

Axelrod-Python/Axelrod

A research tool for the Iterated Prisoner's Dilemma

Language: Python - Size: 8.37 MB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 760 - Forks: 271

tamohannes/urartu

🦁 An open-source NLP framework that offers high-level wrappers designed for effortless launch, enhanced reproducibility, superior control, and unmatched flexibility for your experiments.

Language: Python - Size: 168 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 11 - Forks: 0

michaelflppv/ged-approximation

This is a repository of the code used for the experimental work in my Bachelor thesis on Approximation Algorithms for Graph Edit Distance (GED). It includes implementations, benchmarking scripts, and evaluation methods for comparing GED approximation algorithms with exact computations.

Language: C++ - Size: 206 MB - Last synced at: 10 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 0