Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/cbg-ethz/hdl-x

https://github.com/cbg-ethz/hdl-x

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.4%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: cbg-ethz
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Size: 50.8 KB
Statistics
  • Stars: 3
  • Watchers: 4
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 5 years ago · Last pushed over 5 years ago
Metadata Files
Readme License

README.md

HDL-X

This repository contains all R Markdown files used for the data analysis presented in Cardner et al. (2020), doi: 10.1172/jci.insight.131491.

Main document structure

For reasons of data privacy, this repository contains no actual data, but merely the code used to analyse it. The raw data was collated and stored as tidy data in RDS files under computations/ (not committed). In general, the data frames were stored in a long format, with a column named key coding for the feature (clinical, protein, lipid) and a column named value recording the measurement. A column named Proband ID contained an anonymised subject code.

  • Normalisation
    • Proteomics and lipidomics in OmicsNormalisation.Rmd
    • NMR spectroscopy in Nightingale.Rmd
    • Functional bioassays in FunctionalNormalisation.Rmd
    • Clinical imputation in ClinicalImputation.Rmd
  • Mixed-effects modelling in MixedEffects.Rmd
  • Logistic regression in glmnet.Rmd
  • PLS regression in PLS.Rmd
  • Graphical lasso in HugeNPN.Rmd
  • Helper functions
    • helper_functions.R
    • helper_normalisation.R
    • helper_volcanoes.R

Additional analyses

In addition to the main documents, there are auxiliary R Markdown files for various purposes. Importantly, the JointGGM.Rmd explores the joint graphical lasso.

Owner

  • Name: Computational Biology Group (CBG)
  • Login: cbg-ethz
  • Kind: organization
  • Location: Basel, Switzerland

Beerenwinkel Lab at ETH Zurich

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