Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: reproducible-paper

Repositories

TomMonks/des_sharing_lit_review

Systematic scoping review paper for healthcare DES model sharing.

Language: HTML - Size: 10.4 MB - Last synced: about 23 hours ago - Pushed: 1 day ago - Stars: 2 - Forks: 1

tlnagy/Nagy_2023_SwellMigration

Code used to generate the figures for the "Neutrophils Actively Swell to Potentiate Migration" paper

Language: Julia - Size: 32.6 MB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

benmarwick/rrtools

rrtools: Tools for Writing Reproducible Research in R

Language: R - Size: 4.86 MB - Last synced: 17 days ago - Pushed: 3 months ago - Stars: 664 - Forks: 82

computorg/template-computo-quarto

Template for submitting a manuscript with quarto (Jupyter or Rmarkdown)

Language: TeX - Size: 25 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 9 - Forks: 5

cdcarrion/Marijuana-Law

El Efecto de la Legalización de la Marihuana sobre la Criminalidad en los Estados Unidos

Language: R - Size: 5.02 MB - Last synced: about 1 month ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

apdavison/bulbnet-reproduction

Code associated with the article "[Rp] Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model"

Language: TeX - Size: 13.2 MB - Last synced: about 2 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 1

widdowquinn/SI_Holmes_etal_2020

Supplementary information for Holmes et al. (2020)

Language: HTML - Size: 67.3 MB - Last synced: about 2 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 1

alan-turing-institute/TCPDBench

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

Size: 154 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 123 - Forks: 26

klemenjak/nilm-papers-with-code

An archive for NILM papers with source code and other supplemental material

Size: 29.3 KB - Last synced: 3 months ago - Pushed: 5 months ago - Stars: 123 - Forks: 25

cambridge-mlg/DUN

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

Language: Jupyter Notebook - Size: 34.8 MB - Last synced: 23 days ago - Pushed: 8 months ago - Stars: 71 - Forks: 11

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.

Language: HTML - Size: 15.8 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 618 - Forks: 137

benmarwick/kwakmarwickaas2015

Language: HTML - Size: 3.81 MB - Last synced: 3 months ago - Pushed: about 7 years ago - Stars: 1 - Forks: 0

yufree/pmdda

reproducible repo for PMDDA paper

Language: HTML - Size: 1.25 GB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 5 - Forks: 1

AaronGullickson/markdown_course_materials

Course Materials for Code Horizons Course on Creating Reproducible Reports with Quarto and R Markdown

Language: TeX - Size: 7.61 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 7 - Forks: 7

ReneHeim/proj_on_uav

This repository contains the code to reproduce the article (DOI). The presented method allows to extract oblique and nadir viewing angles from UAV-mounted, multispectral snapshot cameras.

Language: Python - Size: 415 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0

carlosstack/reproducible-research

:tornado: :bar_chart: The basic goal of this project is to explore the NOAA Storm Database and answer some basic questions about severe weather events.

Language: HTML - Size: 579 KB - Last synced: 3 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

nevrome/rrtools.addin

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

Language: R - Size: 1.77 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 17 - Forks: 2

nuest/ten-simple-rules-dockerfiles

Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science

Language: TeX - Size: 19.6 MB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 60 - Forks: 15

carpentries-incubator/quarto-project-example

Project Example for the Lesson: Introduction to Reproducible Publications with Quarto

Language: JavaScript - Size: 2.26 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 5 - Forks: 49

carpentries-incubator/reproducible-publications-quarto

Introduction to Reproducible Publications with Quarto

Language: Python - Size: 78.7 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 9 - Forks: 17

econ-ark/nbreproduce

Reproduce Jupyter Notebooks inside Docker Containers.

Language: Jupyter Notebook - Size: 626 KB - Last synced: 13 days ago - Pushed: 7 months ago - Stars: 10 - Forks: 1

uf-repro/rmarkdown-intro

An Introduction to Writing Reproducible Manuscripts Using RMarkdown

Language: TeX - Size: 340 KB - Last synced: 22 days ago - Pushed: 7 months ago - Stars: 2 - Forks: 0

owenmackwood/pubfig

A simple module for creating publication-quality figures, and recreating them at the press of a button.

Language: Python - Size: 116 KB - Last synced: 5 months ago - Pushed: about 2 years ago - Stars: 4 - Forks: 0

perwin/db-nr_paper

Files and Jupyter notebooks for paper on frequency and sizes of double bars and nuclear rings in local barred galaxies.

Language: Jupyter Notebook - Size: 4.51 MB - Last synced: 5 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

tpilz/paper_drought_prediction_brazil

Analysis scripts of the paper "Seasonal drought prediction for semiarid northeast Brazil: what is the added value of a process-based hydrological model?", published in HESS

Language: R - Size: 67.4 MB - Last synced: 4 months ago - Pushed: about 5 years ago - Stars: 4 - Forks: 1

benmarwick/ktc11

Language: R - Size: 220 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 4

fungenomics/HGG-oncohistones

Analysis for "K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas" (Jessa et al, Nature Genetics, 2022)

Language: HTML - Size: 16.6 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 5 - Forks: 1

alan-turing-institute/memorization

Code for "On Memorization in Probabilistic Deep Generative Models"

Language: Python - Size: 51.8 KB - Last synced: 3 months ago - Pushed: over 2 years ago - Stars: 5 - Forks: 0

zkamvar/Sudden_Oak_Death_in_Oregon_Forests

Population genetic analysis of _Phytophthora ramorum_ data from Oregon forests in Curry County

Language: HTML - Size: 179 MB - Last synced: 8 months ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 3

SchlossLab/Sze_PCRSeqEffects_mSphere_2019

The impact of DNA polymerase and number of rounds of amplification in PCR on 16S rRNA gene sequence data

Language: TeX - Size: 45.6 MB - Last synced: 8 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 5

SchlossLab/Hannigan_ConjunctisViribus_ploscompbio_2018

Using graph database techniques to understand the infectious relationships between bacteria and phages.

Language: PostScript - Size: 449 MB - Last synced: 8 months ago - Pushed: about 6 years ago - Stars: 2 - Forks: 4

SchlossLab/Hannigan_CRCVirome_mBio_2018

Investigating the gut virus communities associated with colon cancer.

Language: PostScript - Size: 53.7 MB - Last synced: 8 months ago - Pushed: over 3 years ago - Stars: 9 - Forks: 7

SchlossLab/Zackular_AbAOMDSS_mSphere_2015

Repository to accompany "Manipulation of the Gut Microbiome Reveals Role for Microbial Community Structure in Colon Tumorigenesis"

Language: R - Size: 31.3 MB - Last synced: 8 months ago - Pushed: over 7 years ago - Stars: 4 - Forks: 0

SchlossLab/Schloss_PacBio16S_PeerJ_2015

Repository to accompany "Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system"

Language: Shell - Size: 1.29 MB - Last synced: 8 months ago - Pushed: over 6 years ago - Stars: 6 - Forks: 2

nuest/reproducible-research-and-giscience

Ready to use R Markdown notebook for the paper "Reproducible research and GIScience: an evaluation using AGILE conference papers"

Language: Dockerfile - Size: 1.16 MB - Last synced: 8 months ago - Pushed: almost 5 years ago - Stars: 3 - Forks: 7

everhartlab/sclerotinia-366

Analysis for "Population structure and phenotypic variation of *Sclerotinia sclerotiorum* from dry bean (*Phaseolus vulgaris*) in the United States"

Language: Shell - Size: 165 MB - Last synced: 8 months ago - Pushed: about 6 years ago - Stars: 10 - Forks: 6

csiro-crop-informatics/repset

Reproducible evaluation of short read mappers

Language: Nextflow - Size: 3.37 MB - Last synced: 8 months ago - Pushed: about 2 years ago - Stars: 2 - Forks: 3

LindaBetz/APMS_NetworkTree

Code for "Disentangling heterogeneity of psychosis expression in the general population: sex-specific moderation effects of environmental risk factors on symptom networks", Psychological Medicine, 2021.

Language: R - Size: 1.1 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

cduvallet/microbiomeHD 📦

Cross-disease comparison of case-control gut microbiome studies

Language: Python - Size: 2.65 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 60 - Forks: 28

tfrank1971/LaTeX_Tutorial_CPT_PSP

LaTeX template files described in the article "LaTeX tutorial for the standardization and automation of population analysis reports"

Language: R - Size: 5.03 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 1

SchlossLab/Jenior_Modeling_mSystems_2017

Repo associated with Jenior et. al. (2017). Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes. mSystems.

Language: R - Size: 373 MB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 1

SchlossLab/Jenior_Metatranscriptomics_mSphere_2018

Repository associated with Jenior ML, et al. (2018). mSphere.

Language: R - Size: 261 MB - Last synced: 9 months ago - Pushed: almost 6 years ago - Stars: 4 - Forks: 2

digantamisra98/Reproducibilty-Challenge-ECANET

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

Language: Python - Size: 78.1 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 31 - Forks: 2

SchlossLab/Sze_CRCMetaAnalysis_mBio_2018

Language: R - Size: 172 MB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 6 - Forks: 3

SchlossLab/Sze_FollowUps_Microbiome_2017

Language: HTML - Size: 100 MB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 3

alan-turing-institute/CSV_Wrangling

Repository for reproducibility of the CSV file project

Language: TeX - Size: 6.2 MB - Last synced: 3 months ago - Pushed: over 2 years ago - Stars: 26 - Forks: 6

eveskew/bayesian_snake_movement

Analyzing snake movement data using Stan models (from R)

Language: R - Size: 568 KB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0

eveskew/frog_chytrid_transcriptomics

Code, data, and figures for an experimental pathogen exposure study using wood frogs and American bullfrogs

Language: R - Size: 129 MB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

pliu55/PRAM_paper

Key results reported by PRAM's manuscript and scripts for reproducibility

Language: R - Size: 11.3 MB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

MartinHinz/bayesian.demographic.reconstruction.2022

Research compendium for ‘Bayesian inference of prehistoric population dynamics from multiple proxies: a case study from the North of the Swiss Alps’

Language: HTML - Size: 111 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 3 - Forks: 0

AntonioFasano/rnw2pdf

Emacs library to convert (reproducible research) Rnw documents to PDFs

Language: Emacs Lisp - Size: 23.4 KB - Last synced: 11 months ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0

jeffreyhanson/genetic-surrogates

Data, code, and results for a research paper investigating surrogates for genetic data in conservation planning

Language: TeX - Size: 490 MB - Last synced: 4 months ago - Pushed: over 4 years ago - Stars: 3 - Forks: 0

SchlossLab/Sze_Obesity_mBio_2016

Language: R - Size: 38 MB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 12 - Forks: 9

egouldo/ReproEcoDecisions

Are conservation and ecological decision support tools reproducible?

Language: TeX - Size: 1.26 MB - Last synced: 4 months ago - Pushed: almost 6 years ago - Stars: 4 - Forks: 1

benmarwick/AP_SC Fork of cylerc/AP_SC

R script for Spirit Cave zooarchaeological analysis.

Language: HTML - Size: 406 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

fbrundu/py_session

Print session information

Language: Python - Size: 17.6 KB - Last synced: 3 days ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1

SchlossLab/Topcuoglu_ML_mBio_2020

Best practices for applying machine learning to bacterial 16S rRNA gene sequencing data

Language: R - Size: 372 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 24 - Forks: 12

jperkel/computed_manuscript

A model executable manuscript

Language: HTML - Size: 6.18 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 44 - Forks: 10

SchlossLab/Sovacool_OptiFit_mSphere_2022 📦

The manuscript accompanying the OptiFit algorithm in mothur

Language: Python - Size: 140 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 2 - Forks: 2

booktrackerGirl/Deep-Learning-Coursework--DropEdge

A coursework done as a part of my MSc module on Deep Learning.

Language: Jupyter Notebook - Size: 8.13 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

miriamspsantos/open-source-imbalance-overlap

A collection of Open Source Contributions in Learning from Imbalanced and Overlapped Data

Size: 7.81 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 4 - Forks: 1

frederic-santos/org-template-ijoa

An org-mode template for writing and submitting scientific articles to the International Journal of Osteoarchaeology

Language: TeX - Size: 269 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

RPanczak/TEMPO_syst-rev

R code and data to reproduce analyses of the systematic review by Panczak et al. (2020). Part of the TEMPO project.

Language: HTML - Size: 18.7 MB - Last synced: over 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

crsh/reproducible-research-practices-workshop

Workshop on reproducible research practices for psychologists

Language: HTML - Size: 71.9 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 15 - Forks: 2

aframosp/AGNView

Reproduction repository for "The viewing angle in AGN SED models, a data-driven analysis"

Language: HTML - Size: 414 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

JoseRZapata/TempoAES42

Results of the paper: Zapata, Jose R.; Gómez, Emilia. "Comparative Evaluation and Combination of Audio Tempo Estimation Approaches", AES 42nd International Conference: Semantic Audio, Ilmenau, Germany. pp. 198 - 207, Jul 2011. in a jupyter notebook

Language: Jupyter Notebook - Size: 4.92 MB - Last synced: over 1 year ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 0

walice/Trade-IFF

Estimates of illicit financial flows due to trade misinvoicing

Language: R - Size: 339 KB - Last synced: over 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

fungenomics/G34-gliomas

Cell-of-origin analysis for "Histone H3.3G34-mutant interneuron progenitors co-opt PDGFRA for gliomagenesis" (Chen*, Deshmukh*, Jessa*, Hadjadj*, et al, Cell, 2020)

Language: HTML - Size: 27.3 MB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

sjessa/chromswitch-analysis

Code and data to accompany the chromswitch paper, "chromswitch: A flexible method for detecting chromatin state switches" (Jessa and Kleinman, Bioinformatics, 2018)

Language: R - Size: 228 MB - Last synced: over 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1

SchlossLab/Schloss_PacBio16S_PeerJ_2016

Repo for Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

Language: TeX - Size: 18.9 MB - Last synced: about 1 year ago - Pushed: about 8 years ago - Stars: 7 - Forks: 1

SchlossLab/Kozich_MiSeqSOP_AEM_2013

Reproducible analysis of sequence analysis on a MiSeq

Language: HTML - Size: 2.64 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 9 - Forks: 3

benmarwick/mjbnaturepaper

Language: R - Size: 102 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 5 - Forks: 0

benmarwick/1989-excavation-report-Madjedbebe

Text, data and code to accompany the analysis of the 1989 excavation data

Language: R - Size: 32.1 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 13 - Forks: 4

SchlossLab/Schubert_AbxD01_mBio_2015

Reproducible workflow for Schubert et al. 2015 mBio

Language: R - Size: 59.4 MB - Last synced: about 1 year ago - Pushed: almost 9 years ago - Stars: 2 - Forks: 3

cambridge-mlg/arch_uncert

Code for "Variational Depth Search in ResNets" (https://arxiv.org/abs/2002.02797)

Language: Jupyter Notebook - Size: 5.92 MB - Last synced: 23 days ago - Pushed: almost 4 years ago - Stars: 9 - Forks: 5

frederic-santos/compendium-santos-2020-jasrep

A research compendium for an article published in JAS:Reports (2020), "Modern methods for old data: An overview of some robust methods for outliers detection with applications in osteology".

Language: TeX - Size: 1.51 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

walice/synth

Constructing a synthetic counterfactual to analyze impact of carbon taxes

Language: R - Size: 164 KB - Last synced: 4 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

docmanny/smRecSearch

Snakemake Implementation of RecSearch featured in "Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk"

Language: HTML - Size: 60.7 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 1