IBD-Network-Models-Reproduction (May 15-17, 2019)

Report

As part of the NLM Reproducibility Workshop, May 15-17, 2019, we tried to reproduce the study published in Nature Genetics volume 49, pages 1437–1449 (2017)

Outline of the group's workflow

IBD-Repro_presentation.ipynb

Reproducing figures

Supplementary Table 15/16 and reproduce Fig2

netweaver.Rmd
├── SupplTable15.csv
├── SupplTable16.csv
    ├──Fig2_repro.pdf

Curating directory path

get_in_and_out.ipynb
├── example.csv

DirectoryNodes_EEM-wPaths.ipynb
├── DirectoryNodes.csv
├── NodeTypes_wPaths.csv

Visualization

├── DirectoryNodes_wPaths.csv
├── NodeTypes_wPaths.csv
├── repotree.py
├── repotree.ipynb
├── PAPER_DATA-rt-ig.html
├── tree04.html
├── requirements.txt

Directories Tree via Fruchterman-Reingold Layout

tree04.html

Directories Tree via Reingold-Tilford Layout

PAPER_DATA-rt-ig.html

Code

├── repotree.py  - visualization for Reingold-Tilford Layout
├── repotree.ipynb
├── PAPER_DATA-rt-ig.html
├── tree04.html
├── requirements.txt - for repotree.py

Visualization legend:

red - code
blue - data (ASCII)
green - data (binary)
black - directories
magenta - everything else