Ecosyste.ms: Awesome

https://github.com/showyourwork/showyourwork

A workflow for reproducible and open scientific articles

continuous-integration latex open-source reproducible-research reproducible-science scientific-papers scientific-workflows

Last synced: 03 Jul 2024

https://github.com/VIDA-NYU/reprozip

ReproZip is a tool that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.

archiving computational-science docker hacktoberfest linux nyu ptrace python reproducibility reproducible-research reproducible-science reprounzip reprozip science scientific-computing vagrant

Last synced: 02 Jul 2024

https://github.com/JunoLab/Weave.jl

Scientific reports/literate programming for Julia

julia literate-programming reproducible-research scientific-reports scientific-workflows

Last synced: 28 Jun 2024

https://github.com/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.

cpp hacktoberfest image-analysis insight-toolkit itk medical-imaging numfocus open-science open-source python reproducible-research scientific-computing

Last synced: 27 Jun 2024

http://ropensci.github.io/reproducibility-guide

:no_entry: ARCHIVED :no_entry:

reproducibility reproducibility-guide reproducible-research

Last synced: 25 Jun 2024

https://github.com/cthoyt/drugbank_downloader

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

drugbank python reproducible-research

Last synced: 23 Jun 2024

https://github.com/ropensci-books/drake

The user manual for the drake R package

data-science drake high-performance-computing makefile pipeline r reproducibility reproducible-research ropensci rstats workflow

Last synced: 21 Jun 2024

https://github.com/timtroendle/cookiecutter-reproducible-research

A cookiecutter template for reproducible research projects using Python, Snakemake, and Pandoc.

automation cluster-computing cookiecutter-template pandoc python reproducible-research snakemake

Last synced: 21 Jun 2024

https://github.com/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.

biomedical-engineering brain-connectivity-analysis brain-research computational-neuroscience connectomics data-analysis data-science data-visualization deep-learning graph-theory machine-learning matlab network-analysis neuroimaging neuroscience open-source reproducible-research research-tools scientific-software toolbox

Last synced: 20 Jun 2024

https://github.com/nipy/workshops

Brain imaging workshops

neuroimaging python reproducible-research

Last synced: 20 Jun 2024

https://github.com/ropensci/drake

An R-focused pipeline toolkit for reproducibility and high-performance computing

data-science drake high-performance-computing makefile peer-reviewed pipeline r r-package reproducibility reproducible-research ropensci rstats workflow

Last synced: 17 Jun 2024

https://github.com/fbrundu/py_session

Print session information

computational-biology data-science modules packages python3 reproducibility reproducible reproducible-experiments reproducible-paper reproducible-research reproducible-science session

Last synced: 17 Jun 2024

https://github.com/nuest/ten-simple-rules-dockerfiles

Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science

containerisation containerization dockerfiles open-science reproducible-paper reproducible-research reproducible-science ten-simple-rules

Last synced: 16 Jun 2024

https://github.com/gpoore/codebraid

Live code in Pandoc Markdown

bash javascript julia-language literate-programming markdown pandoc-filter pandoc-markdown python r-language reproducible-analysis reproducible-research reproducible-workflows rust rust-lang

Last synced: 16 Jun 2024

https://github.com/henripal/labnotebook

LabNotebook is a tool that allows you to flexibly monitor, record, save, and query all your machine learning experiments.

experiment-manager experimental-data machine-learning postgres postgresql python reproducibility reproducible-research vuejs webapp

Last synced: 14 Jun 2024

https://github.com/orfeotoolbox/OTB

Github mirror of https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb

cpp14 image-processing open-science open-source orfeotoolbox osgeo otb remote-sensing reproducible-research

Last synced: 12 Jun 2024

https://github.com/sgibson91/binderhub-deploy

Deploy a BinderHub from scratch on Microsoft Azure

azure binder binderhub cloud docker hut23 reproducibility reproducible-research

Last synced: 10 Jun 2024

https://github.com/rostools/prodigenr

Project directory generator R package

cran devtools open-science open-source project-management reproducibility reproducible-research reproducible-science rstats rstudio usethis

Last synced: 10 Jun 2024

https://github.com/markvanderloo/lumberjack

Track changes in data with ease

daff datascience logging r reproducible-research

Last synced: 10 Jun 2024

https://github.com/reprohack/reprohack-hq

ReproHack Headquarters

hackathon reproducible-research reresearch-code-review

Last synced: 10 Jun 2024

https://github.com/baumer-lab/fertile

creating optimal conditions for reproducibility

r reproducibility reproducible-research tidyverse workflow

Last synced: 10 Jun 2024

https://github.com/neuhausi/canvasXpress

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

analytics bioinformatics chart charting cran dash dashboard data-analytics data-science data-visualization genomics graphs javascript network network-visualization python r reproducible-research shiny visualization

Last synced: 10 Jun 2024

https://github.com/hofnerb/papeR

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

cran knitr latex r-language r-package reporting reproducible reproducible-research sweave

Last synced: 10 Jun 2024

https://github.com/parklab/nozzle

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

gehlenborglab html-report reproducible-research

Last synced: 10 Jun 2024

https://github.com/rubenarslan/repro_web_stack

The stack I use to make reproducible reports of my statistical analyses

knitr markdown r reproducibility reproducible-research reproducible-science rmarkdown statistics zenodo

Last synced: 10 Jun 2024

https://github.com/jdblischak/reproducible-research-ctv

**Archived** CRAN Task View: Reproducible Research

cran r reproducibility reproducible-research rstats task-view

Last synced: 10 Jun 2024

https://github.com/nevrome/rrtools.addin

R Package - A graphical user interface for some of the main functions of Ben Marwick's rrtools package

r reproducible-paper reproducible-research rstudio-addin

Last synced: 10 Jun 2024

https://github.com/NCEAS/recordr

Provenance tracking for R.

provenance r reproducible-research

Last synced: 10 Jun 2024

https://github.com/jasenfinch/projecttemplates

R project templates for reproducible research and analyses

r reproducibility reproducible-research reproducible-science research-project research-tool

Last synced: 10 Jun 2024

https://github.com/testlnord/rdstemplate

Reproducible Data Science RStudio Project Template

data-science r reproducibility reproducible-research rstudio template

Last synced: 10 Jun 2024

https://github.com/holmesjoli/utilsR

R utility functions

r reproducibility reproducible-analysis reproducible-research reproducible-workflows

Last synced: 10 Jun 2024

https://github.com/holmesjoli/archiveR

An R package for data archiving and linking with code

archive git r reproducibility reproducible-analysis reproducible-research reproducible-workflows

Last synced: 10 Jun 2024

https://github.com/nt-williams/cabinets

:package: for custom file structure templates accessible in R sessions outside the ones they were created in.

reproducible-research workflow workflow-automation

Last synced: 10 Jun 2024

https://github.com/seabbs/prettypublisher

R package to help in formatting R markdown documents into a publishable format

publishing r-package r-stats reproducible-research

Last synced: 10 Jun 2024

https://github.com/CredibilityLab/groundhog

Reproducible R Scripts Via Date Controlled Installing & Loading of CRAN & Git Packages

cran r r-package reproducible-research rstats

Last synced: 10 Jun 2024

https://github.com/ropensci/targets

Function-oriented Make-like declarative workflows for R

data-science high-performance-computing make peer-reviewed pipeline r r-package r-targetopia reproducibility reproducible-research rstats targets workflow

Last synced: 09 Jun 2024

https://github.com/nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

annotation bioinformatics cancer conda containers gatk4 genomics germline next-generation-sequencing nextflow nf-core pipeline pre-processing reproducible-research somatic target-panels variant-calling whole-exome-sequencing whole-genome-sequencing workflow

Last synced: 08 Jun 2024

https://github.com/alan-turing-institute/AnnotateChange

A simple flask application to collect annotations for the Turing Change Point Dataset, a benchmark dataset for change point detection algorithms

bootstrap change-detection changepoint changepoint-detection d3-visualization d3js d3v5 flask flask-application flask-login flask-sqlalchemy open-science reproducible-research time-series time-series-analysis

Last synced: 08 Jun 2024

https://github.com/alan-turing-institute/TCPDBench

The Turing Change Point Detection Benchmark: An Extensive Benchmark Evaluation of Change Point Detection Algorithms on real-world data

benchmark benchmark-suite change-detection change-point change-point-detection changepoint reproducible-paper reproducible-research reproducible-science

Last synced: 08 Jun 2024

https://github.com/jupyter-guide/ten-rules-jupyter

Ten Simple Rules for Writing and Sharing Computational Analyses in Jupyter Notebooks

binder jupyter jupyter-lab jupyter-notebook machine-learning reproducible-research

Last synced: 07 Jun 2024

https://github.com/mpastell/Pweave

Pweave is a scientific report generator and a literate programming tool for Python. It can capture the results and plots from data analysis and works well with numpy, scipy and matplotlib.

jupyter python python3 reproducible-research scientific-reports

Last synced: 06 Jun 2024

https://github.com/Pakillo/Rmarkdown_tutorial

Reproducible Research with Rmarkdown: data management, analysis, and reporting all-in-one

reproducible-research rmarkdown slide

Last synced: 04 Jun 2024

https://github.com/wlandau/targets-shiny

Example Shiny app containing a targets pipeline.

high-performance-computing make pipeline r reproducibility reproducible-research shiny targets workflow

Last synced: 04 Jun 2024

https://github.com/wlandau/targets-tutorial

Short course on the targets R package

data-science make pipeline r r-package reproducibility reproducible-research rstats targets workflow

Last synced: 04 Jun 2024

https://github.com/ropensci/daiquiri

Data quality reporting for temporal datasets.

data-quality initial-data-analysis r r-package reproducible-research rstats temporal-data time-series

Last synced: 03 Jun 2024

https://github.com/FRBCesab/rcompendium

:package: Create a package or compendium structure

package r reproducible-research research-compendium

Last synced: 03 Jun 2024

https://github.com/datasnakes/renv

Creating virtual environments for R.

biohackathon cli hackathon package-management project-environment python r renv reproducible-research virtual-environment

Last synced: 03 Jun 2024

https://github.com/tweag/funflow

Functional workflows

content-addressable-storage reproducible-research workflow

Last synced: 02 Jun 2024

https://github.com/htm-community/htm.core

Actively developed Hierarchical Temporal Memory (HTM) community fork (continuation) of NuPIC. Implementation for C++ and Python

ai anomaly-detection cortical-learning cpp hierarchical-temporal-memory htm neural-networks neuromorphic-computing neuroscience neuroscience-inspired-ai nupic prediction reproducible-research sparse-distributed-memory

Last synced: 28 May 2024

https://github.com/ctuning/ck-env

CK repository with components and automation actions to enable portable workflows across diverse platforms including Linux, Windows, MacOS and Android. It includes software detection plugins and meta packages (code, data sets, models, scripts, etc) with the possibility of multiple versions to co-exist in a user or system environment.

android codereef collective-knowledge compilers datasets hpc libraries linux macos mobile-devices models multiple-versions package-manager portable-workflows python reproducible-research research-workflows tools windows

Last synced: 28 May 2024

https://github.com/cthoyt/chembl-downloader

Write reproducible code for getting and processing ChEMBL

bioinformatics chembl cheminformatics chemogenomics chemometrics machine-learning pharmacology proteochemometrics python reproducible-research toxicology

Last synced: 27 May 2024

https://github.com/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.

atac-seq bioinformatics bioinformatics-pipeline chip-seq fastq ngs pipeline reproducible-research rna-seq snakemake sra workflows

Last synced: 24 May 2024

https://github.com/Pakillo/rmdTemplates

Rmarkdown templates for reproducible science

r reproducible-research rmarkdown rmarkdown-templates rstudio

Last synced: 24 May 2024

https://github.com/ropensci/lightr

Import spectral data and related metadata in R

file-import r r-package reproducibility reproducible-research reproducible-science spectral-data spectroscopy

Last synced: 21 May 2024

https://github.com/JavierAntoran/Bayesian-Neural-Networks

Pytorch implementations of Bayes By Backprop, MC Dropout, SGLD, the Local Reparametrization Trick, KF-Laplace, SG-HMC and more

approximate-inference bayes-by-backprop bayesian-inference bayesian-neural-networks classification deep-learning hmc kronecker-factored-approximation langevin-dynamics local-reparametrization-trick mc-dropout mcmc out-of-distribution-detection pytorch regression reproducible-research sgld uncertainty uncertainty-neural-networks variational-inference

Last synced: 21 May 2024

https://github.com/Rapporter/pander

An R Pandoc Writer: Convert arbitrary R objects into markdown

literate-programming markdown pandoc pandoc-markdown r reproducible-research rmarkdown

Last synced: 20 May 2024

https://github.com/crsh/papaja

papaja (Preparing APA Journal Articles) is an R package that provides document formats to produce complete APA manuscripts from RMarkdown-files (PDF and Word documents) and helper functions that facilitate reporting statistics, tables, and plots.

apa apa-guidelines journal manuscript psychology r r-package reproducible-paper reproducible-research rmarkdown

Last synced: 20 May 2024

https://github.com/benmarwick/researchcompendium

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

compendium reproducibility reproducible-research reproducible-science

Last synced: 20 May 2024

https://github.com/leeper/make-example

An example of using make for a data analysis project

data-analysis make manuscript reproducible-research

Last synced: 20 May 2024

https://github.com/hughjonesd/huxtable

An R package to create styled tables in multiple output formats, with a friendly, modern interface.

cran html huxtable latex microsoft-word powerpoint r reproducible-research tables

Last synced: 20 May 2024

https://github.com/nanxstats/liftr

🐳 Containerize R Markdown documents for continuous reproducibility

containerization docker dynamic-documents knitr liftr reproducible-research reproducible-science rmarkdown statistical-computing

Last synced: 20 May 2024

https://github.com/ropensci/osfr

R interface to the Open Science Framework (OSF)

open-science osf reproducible-research

Last synced: 20 May 2024

https://github.com/wlandau/drake-examples

Example workflows for the drake R package

data-science drake high-performance-computing makefile pipeline r reproducibility reproducible-research ropensci rstats workflow

Last synced: 20 May 2024

https://github.com/wlandau/targets-minimal

A minimal example data analysis project with the targets R package

data-science high-performance-computing pipeline r reproducibility reproducible-research rstats statistics targets workflow

Last synced: 20 May 2024

https://github.com/strazto/mandrake

📖🐉- Bring reading the manual 📖 closer to your drake 🐉 workflow 🔥

data-science drake high-performance-computing makefile pipeline r r-package reproducibility reproducible-research rstats workflow

Last synced: 20 May 2024

https://github.com/ropensci/gittargets

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

data-science data-version-control data-versioning r r-package reproducibility reproducible-research rstats targets workflow

Last synced: 19 May 2024

https://github.com/Netflix/metaflow

:rocket: Build and manage real-life ML, AI, and data science projects with ease!

ai aws azure data-science datascience gcp high-performance-computing kubernetes machine-learning ml ml-infrastructure ml-platform mlops model-management productivity python r r-package reproducible-research rstats

Last synced: 19 May 2024

https://github.com/clementchadebec/benchmark_VAE

Unifying Variational Autoencoder (VAE) implementations in Pytorch (NeurIPS 2022)

benchmarking beta-vae comparison normalizing-flows pixel-cnn pytorch reproducibility reproducible-research vae vae-gan vae-implementation vae-pytorch variational-autoencoder vq-vae wasserstein-autoencoder

Last synced: 17 May 2024

https://github.com/PredictiveEcology/reproducible

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

r-package reproducibility reproducible-research

Last synced: 16 May 2024

https://github.com/benmarwick/rrtools

rrtools: Tools for Writing Reproducible Research in R

quarto quarto-template r reproducibility reproducible-paper reproducible-research reproducible-science research-compendium research-paper research-project research-tool

Last synced: 16 May 2024

https://github.com/binder-examples/stencila-py

Demo for Stencila & DAR on binder with Python code

binder binder-ready python reproducible-research stencila

Last synced: 16 May 2024

https://github.com/Audio-WestlakeU/FullSubNet

PyTorch implementation of "FullSubNet: A Full-Band and Sub-Band Fusion Model for Real-Time Single-Channel Speech Enhancement."

audio band denoising full-band narrow-band noise-reduction paper pretrained-model pytorch reproducible-research single-channel speech speech-enhancement speech-processing speech-separation sub-band

Last synced: 15 May 2024

https://github.com/ropensci/git2rdata

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

r r-package reproducible-research rstats version-control

Last synced: 14 May 2024

https://github.com/rubenarslan/formr.org

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

experience-sampling feedback formr javascript knitr opencpu php reproducible-research survey surveys

Last synced: 13 May 2024

https://github.com/Kaixhin/FGLab

Future Gadget Laboratory

machine-learning reproducible-research reproducible-science

Last synced: 13 May 2024

https://github.com/minerva-ml/open-solution-googleai-object-detection

Open solution to the Google AI Object Detection Challenge :maple_leaf:

challenge data-science deep-learning deep-neural-networks detection-network google-ai-challange machine-learning mask-rcnn object-detection pipeline pipeline-framework reproducibility reproducible-experiments reproducible-research retina-net

Last synced: 12 May 2024

https://github.com/minerva-ml/steppy

Lightweight, Python library for fast and reproducible experimentation :microscope:

data-science deep-learning image-processing machine-learning minimal-interface nlp open-source pipeline python python-library python3 reproducibility reproducible-research steppy steppy-library steppy-toolkit steps

Last synced: 12 May 2024

https://github.com/minerva-ml/steppy-toolkit

Curated set of transformers that make your work with steppy faster and more effective :telescope:

data-science deep-learning keras keras-models machine-learning nlp open-source pipeline pipeline-framework python python3 pytorch pytorch-models reproducibility reproducible-research steppy steppy-toolkit steps tensorflow tensorflow-models

Last synced: 12 May 2024

https://github.com/iterative/example-get-started

Get started DVC project (NLP, random forest)

dvc example machine-learning nlp python random-forest reproducibility reproducible reproducible-research

Last synced: 09 May 2024

https://github.com/openplantpathology/OpenPlantPathology

Open Plant Pathology website

openplantpathology reproducible-research

Last synced: 08 May 2024

https://github.com/weecology/portalcasting

Model development, deployment, and evaluation for forecasting Portal ecosystem dynamics

ecology forecasting portal r r-package r-stats reproducible-research shiny workflow

Last synced: 08 May 2024

https://github.com/fmalmeida/bacannot

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

annotation antimicrobial-genes-annotation barrnap genome-analysis genome-browser genomic-islands-prediction insertion-sequences ko-annotation methylation-annotation mobile-genetic-elements nextflow phigaro pipeline prophage-sequences-prediction prophages reproducible-research rgi rrna-prediction virulence-factor virulence-genes

Last synced: 08 May 2024

https://github.com/fmalmeida/ngs-preprocess

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

bax2bam bioinformatics illumina nanopack nextflow ngs ngs-preprocess pacbio pacbio-ccs pipeline porechop reproducible-research reproducible-science trimgalore workflow

Last synced: 08 May 2024

https://github.com/nextflow-io/nextflow

A DSL for data-driven computational pipelines

aws bioinformatics cloud dataflow docker groovy hello hpc nextflow pipeline pipeline-framework reproducible-research reproducible-science sge singularity singularity-containers slurm workflow-engine

Last synced: 08 May 2024

https://github.com/leipzig/awesome-reproducible-research

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

awesome awesome-list reproducibility reproducible-analysis reproducible-research reproducible-science reproducible-workflows

Last synced: 07 May 2024

https://github.com/jimjam-slam/talk-runapp-quarto-2022

julia literate-programming observable-js ojs python qmd quarto r reproducible-reports reproducible-research rstats

Last synced: 07 May 2024

https://github.com/InsightSoftwareConsortium/itkwidgets

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

image-analysis imaging insight-toolkit itk jupyter jupyter-widget jupyterlab-extension kitware medical-visualization meshes open-science open-source point-cloud python reproducible-research scientific-computing scientific-visualization

Last synced: 06 May 2024

https://github.com/stencila/stencila

Programmable, reproducible, interactive documents

document executable interactive programmable reactive reproducible-research

Last synced: 06 May 2024

https://github.com/riatecom/cartostats

Reproducible Cartography

cartography map r r-spatial r-stats reproducible-research

Last synced: 01 May 2024

https://github.com/ddsjoberg/gtsummary

Presentation-Ready Data Summary and Analytic Result Tables

easy-to-use gt html5 r r-package regression-models reproducibility reproducible-research rstats statistics summary-statistics summary-tables table1 tableone

Last synced: 01 May 2024

https://github.com/IDSIA/sacred

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

infrastructure machine-learning mongodb python reproducibility reproducible-research reproducible-science

Last synced: 28 Apr 2024

https://github.com/data-datum/learning_R

List of resources for learning R

books data-manipulation data-visualization datatable dplyr functions ggplot2 purrr r r-programming r-spatial reproducible-research rmarkdown rstudio shiny shiny-apps strings strings-manipulation tidyr webinars

Last synced: 22 Apr 2024

https://github.com/openplantpathology/Reproducibility_in_Plant_Pathology

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.

open-science plant-pathology r reproducible-research reproducible-science research-compendium rstats