benmarwick/rrtools

rrtools: Tools for Writing Reproducible Research in R

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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.

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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 at: about 2 months ago - Pushed at: over 2 years ago - Stars: 139 - Forks: 28

klemenjak/nilm-papers-with-code

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

Size: 29.3 KB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 135 - 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 at: about 1 year ago - Pushed at: over 1 year ago - Stars: 71 - Forks: 11

nuest/ten-simple-rules-dockerfiles

Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science

Language: TeX - Size: 19.6 MB - Last synced at: 9 days ago - Pushed at: over 4 years ago - Stars: 65 - Forks: 15

cduvallet/microbiomeHD 📦

Cross-disease comparison of case-control gut microbiome studies

Language: Python - Size: 2.65 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 60 - Forks: 28

jperkel/computed_manuscript

A model executable manuscript

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digantamisra98/Reproducibilty-Challenge-ECANET

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

Language: Python - Size: 78.1 MB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 31 - Forks: 2

alan-turing-institute/CSV_Wrangling

Repository for reproducibility of the CSV file project

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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 at: 6 months ago - Pushed at: almost 5 years ago - Stars: 28 - Forks: 14

crsh/reproducible-research-practices-workshop

Workshop on reproducible research practices for psychologists

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carpentries-incubator/reproducible-publications-quarto

Introduction to Reproducible Publications with Quarto

Language: Python - Size: 78.7 MB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 17 - Forks: 26

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 at: about 2 months ago - Pushed at: over 2 years ago - Stars: 17 - Forks: 2

benmarwick/mjbtramp

Language: TeX - Size: 276 MB - Last synced at: 3 months ago - Pushed at: about 8 years ago - Stars: 17 - Forks: 9

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 at: about 2 months ago - Pushed at: over 7 years ago - Stars: 15 - Forks: 4

SchlossLab/Baxter_glne007Modeling_GenomeMed_2015

Microbiota-based model improves the sensitivity for detecting colonic lesions

Language: R - Size: 47.2 MB - Last synced at: about 2 years ago - Pushed at: almost 9 years ago - Stars: 14 - Forks: 9

SchlossLab/Sze_Obesity_mBio_2016

Language: R - Size: 38 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 12 - Forks: 9

econ-ark/nbreproduce

Reproduce Jupyter Notebooks inside Docker Containers.

Language: Jupyter Notebook - Size: 626 KB - Last synced at: about 16 hours ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 1

computorg/template-computo-quarto

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

Language: TeX - Size: 25.1 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 9 - Forks: 5

SchlossLab/Kozich_MiSeqSOP_AEM_2013

Reproducible analysis of sequence analysis on a MiSeq

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SchlossLab/Hannigan_CRCVirome_mBio_2018

Investigating the gut virus communities associated with colon cancer.

Language: PostScript - Size: 53.7 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 9 - Forks: 7

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 at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 9 - Forks: 5

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 at: 9 days ago - Pushed at: about 7 years ago - Stars: 9 - Forks: 6

AaronGullickson/markdown_course_materials

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

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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)

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carpentries-incubator/quarto-project-example

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

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acfrery/Grading-Reproducibility-in-Remote-Sensing-Articles

Position Paper for the J-STARS Special Issue on Reproducible Research in Remote Sensing

Language: TeX - Size: 8.43 MB - Last synced at: 9 months ago - Pushed at: almost 5 years ago - Stars: 7 - Forks: 1

SchlossLab/Schloss_PacBio16S_PeerJ_2016

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

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SchlossLab/Sze_CRCMetaAnalysis_mBio_2018

Language: R - Size: 172 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 6 - Forks: 3

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 at: over 1 year ago - Pushed at: over 7 years ago - Stars: 6 - Forks: 2

ReneHeim/proj_on_uav

This repository contains the code to reproduce the article (https://doi.org/10.1007/s11119-024-10133-0). The presented method allows to extract oblique and nadir viewing angles from UAV-mounted, multispectral snapshot cameras.

Language: Python - Size: 12.6 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 5 - Forks: 3

benmarwick/mjbnaturepaper

Language: R - Size: 102 MB - Last synced at: about 2 months ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 0

alan-turing-institute/memorization

Code for "On Memorization in Probabilistic Deep Generative Models"

Language: Python - Size: 51.8 KB - Last synced at: 27 days ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 0

yufree/pmdda

reproducible repo for PMDDA paper

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ctuning/ck-scc

The procedures and a workflow to prepare Student Cluster Competition submissions:

Language: Python - Size: 27.3 KB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 1

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’

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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 at: over 1 year ago - Pushed at: about 3 years ago - Stars: 4 - Forks: 0

miriamspsantos/open-source-imbalance-overlap

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

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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 at: 3 months ago - Pushed at: over 5 years ago - Stars: 4 - 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 at: 12 months ago - Pushed at: about 6 years ago - Stars: 4 - Forks: 1

SchlossLab/Jenior_Metatranscriptomics_mSphere_2018

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

Language: R - Size: 261 MB - Last synced at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 4 - Forks: 2

egouldo/ReproEcoDecisions

Are conservation and ecological decision support tools reproducible?

Language: TeX - Size: 1.26 MB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 4 - Forks: 1

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 at: over 1 year ago - Pushed at: over 8 years ago - Stars: 4 - Forks: 0

perwin/s4g_barfractions

Data files, code, and Jupyter notebooks for paper on frequency of bars in spiral galaxies, using S4G data

Language: Jupyter Notebook - Size: 4.35 MB - Last synced at: 3 months ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 1

fbrundu/py_session

Print session information

Language: Python - Size: 17.6 KB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1

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 at: over 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1

reproindex/ck-reproindex

The index of reproduced papers with reusable research components and unified workflows in the Collective Knowledge format

Language: Python - Size: 1.31 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 3

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 at: about 2 months ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 7

Pakillo/exclosures-Almoraima

Research compendium for "Impactos de la herbivoría por ungulados en las comunidades de plantas leñosas del Parque Natural Los Alcornocales""

Language: TeX - Size: 1.89 MB - Last synced at: 5 days ago - Pushed at: almost 7 years ago - Stars: 3 - Forks: 0

SchlossLab/Schloss_Cluster_PeerJ_2015

Replication study of He et al. (2015) in Microbiome by Pat Schloss & Sarah Westcott

Language: TeX - Size: 3.6 MB - Last synced at: about 2 years ago - Pushed at: almost 9 years ago - Stars: 3 - Forks: 1

SchlossLab/Baxter_WildMice_AEM_2014

R notebook describing data analysis for "Intra- and inter-individual variation masks inter-species variation in the microbiota of sympatric Peromyscus populations"

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TomMonks/des_sharing_lit_review

Systematic scoping review paper for healthcare DES model sharing.

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uf-repro/rmarkdown-intro

An Introduction to Writing Reproducible Manuscripts Using RMarkdown

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SchlossLab/Sovacool_OptiFit_mSphere_2022 📦

The manuscript accompanying the OptiFit algorithm in mothur

Language: Python - Size: 140 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 2

csiro-crop-informatics/repset

Reproducible evaluation of short read mappers

Language: Nextflow - Size: 3.37 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 3

aframosp/AGNView

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

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pliu55/PRAM_paper

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

Language: R - Size: 11.3 MB - Last synced at: 10 months ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

perwin/s4g_barsizes

Files and Jupyter notebooks for paper on sizes of bars in spiral galaxies, using S4G data

Language: Jupyter Notebook - Size: 2.27 MB - Last synced at: 3 months ago - Pushed at: over 5 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 at: over 2 years ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 0

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 at: over 1 year ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 4

jeffreyhanson/raptr-manuscript

Data, code, and results for the raptr R package manuscript

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benmarwick/olympicdamboundaries

Language: R - Size: 222 MB - Last synced at: 3 months ago - Pushed at: almost 8 years ago - Stars: 2 - Forks: 0

SchlossLab/Westcott_OptiClust_mSphere_2017

Paper describing opticlust method published in mSphere

Language: PostScript - Size: 10.9 MB - Last synced at: over 1 year ago - Pushed at: over 8 years ago - Stars: 2 - Forks: 1

benmarwick/Pleistocene-aged-stone-artefacts-from-Jerimalai--East-Timor

Text, data and code to accompany the analysis of stone artefacts reported in Marwick et al.

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SchlossLab/Schubert_AbxD01_mBio_2015

Reproducible workflow for Schubert et al. 2015 mBio

Language: R - Size: 59.4 MB - Last synced at: about 2 years ago - Pushed at: almost 10 years ago - Stars: 2 - Forks: 3

fungenomics/NB-FOXR2

Analysis for "FOXR2 targets LHX6+/DLX+ neural lineages to drive CNS neuroblastoma" (Jessa*, De Cola*, Chandarana*, et al, Cancer Research, 2025)

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benmarwick/ktc11

Language: R - Size: 220 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 4

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 at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

walice/Trade-IFF

Estimates of illicit financial flows due to trade misinvoicing

Language: R - Size: 339 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - 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 at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 1

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 at: about 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

discindo/booklet

Водич за најдобри пракси за повторлива обработка на податоци. A guide for best practices in reproducible data analysis (in Macedonian).

Language: HTML - Size: 4.77 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 1

paezha/Neighborhood-Perceptions-and-Active-Travel-in-Bangladesh

Jamal, S., Mohiuddin, H., Paez, A. (2020) How do the perceptions of neighborhood conditions impact active transportation? A study in Rajshahi, Bangladesh, Transportation Research Part D: Transport and Environment, 87:102525

Language: TeX - Size: 1.57 MB - Last synced at: 3 months ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

Pakillo/Carex.bipolar

Research compendium for "Niche shifts after long-distance dispersal events in bipolar sedges (Carex, Cyperaceae)"

Language: R - Size: 16.2 MB - Last synced at: 5 days ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

manaakiwhenua/manaakiwhenua-manifesto

A manifesto and code publishing framework for the Manaaki Whenua - Landcare Research GitHub account

Language: TeX - Size: 403 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

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 at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

AntonioFasano/rnw2pdf

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

Language: Emacs Lisp - Size: 23.4 KB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0

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 at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 5

benmarwick/datacitation

Research compendium for our paper in 'Advances in Archaeological Practice'

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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 at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 1

SchlossLab/Schloss_PrePrints_mBio_2017

Language: TeX - Size: 9.98 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 1

SchlossLab/Baxter_FITs_Microbiome_2016

Language: Shell - Size: 25.6 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 5

eveskew/bayesian_snake_movement

Analyzing snake movement data using Stan models (from R)

Language: R - Size: 568 KB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

SchlossLab/Sze_FollowUps_Microbiome_2017

Language: HTML - Size: 100 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 3

benmarwick/kwakmarwickaas2015

Language: HTML - Size: 3.81 MB - Last synced at: 3 months ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 0

benmarwick/Steele_et_al_VR003_MSA_Pigments

Language: R - Size: 11.6 MB - Last synced at: 3 months ago - Pushed at: over 9 years ago - Stars: 1 - Forks: 0

benmarwick/Particle-size-analysis-Putslaagte-1

Text, data and code to accompany the particle size analysis reported in Mackay et al. 2014 http://dx.doi.org/10.1016/j.quaint.2014.05.007

Size: 15 MB - Last synced at: 3 months ago - Pushed at: about 11 years ago - Stars: 1 - Forks: 1

Gaglia88/gsm_repro

Reproducibility experiments for Generalized Supervised Meta-blocking

Language: Python - Size: 60.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

karlolukic/reproducibility-of-whotracks.me-paper

This repository contains R code to reproduce Results section from the WhoTracks.me 2018 paper.

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petebachant/repro-qiu-et-al-2024

Reproducing the results of Qiu et al. (2024) "Decarbonized energy system planning with high-resolution..."

Language: Python - Size: 2.94 MB - Last synced at: 6 days ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

nrybowski/ns3-sim

Artefacts for the paper "Evaluating OSPF Convergence with ns-3 DCE"

Language: C++ - Size: 180 KB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

TAOGenna/pytorch-neural-style-transfer

Reconstruction of the original paper on neural style transfer (Gatys et al.)

Language: Jupyter Notebook - Size: 20 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

Faisalse/IntentAware_topn

This is the official repository of the paper "Are we really making much progress? An analysis of intent-aware recommendation models"

Language: Python - Size: 122 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

marcocosta97/grafite-experiments

An automated way to reproduce the results of the paper "Grafite: Taming Adversarial Queries with Optimal Range Filters"

Language: Shell - Size: 23.4 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

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 at: 8 months ago - Pushed at: about 1 year ago - Stars: 0 - 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 at: 7 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

perwin/barprofiles_paper

Files and Jupyter notebooks for paper on bar major-axis profiles

Language: Jupyter Notebook - Size: 17.3 MB - Last synced at: 7 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

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 at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

perwin/n4608-n4643

Files and code for reproducing analysis and figures in Erwin et al. (2020) paper on NGC 4608 and NGC 4643.

Language: Jupyter Notebook - Size: 157 MB - Last synced at: 7 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0