8000 LudvigOlsen (Ludvig Renbo Olsen) · GitHub
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Achievement: Pull Sharkx2Achievement: StarstruckAchievement: Arctic Code Vault Contributor

Achievements

Achievement: Pull Sharkx2Achievement: StarstruckAchievement: Arctic Code Vault Contributor

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LudvigOlsen/README.md

Welcome! I'm Ludvig Olsen

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I'm an R and python developer with a PhD in bioinformatics, working as a Postdoc at the Department of Molecular Medicine (MOMA) at Aarhus University Hospital. Current projects revolve around detection and localization of cancers from cell-free DNA in blood samples.

I worked with deep learning on text at UNSILO and medical imaging data at Cercare Medical.

The aim of my career is to have a very big positive impact on this world of ours! 🌍

R packages

I have developed a set of open source R and Python packages:

groupdata2

  • Divide data into groups
  • Create balanced partitions and cross-validation folds
  • Perform time series windowing
  • Balance existing groups with up- and downsampling


Read more



cvms

  • Cross-validate regression and classification models
  • Evaluate predictions with a tidy output
  • Extract challenging observations
  • Find baselines for a wide range of metrics


Read more



rearrr

  • Rearrrange data points
    - center max value, roll elements, shuffle hierarchy, ...
  • Mutate data points
    - rotate, swirl, cluster, roll values, ...
  • Scaling and measuring utilities
    - MinMax scaling, find angle, find centroid, ...


Read more

xpectr

  • Generate testthat tests
  • RStudio addins for faster development


Read more

Python packages

lionheart

  • Detect pan-cancer from whole genome sequenced cell-free DNA
  • Correlates fragment coverage with chromatin accessibility of 487 cell types
  • Use the trained model or train your own

Read more



nattrs

  • Get, set, mutate, update, or delete nested attributes
  • Works on dict members and object attributes interchangebly
  • Allows regex-based matching on attribute / key names

Read more



generalize

  • Run repeated nested leave-one-dataset-out cross-validation
  • Evaluate predictions with a range of metrics
  • Evaluate univariate models
  • Classes for handling ROC curves and confusion matrices

Read more

GitHub stats

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  1. groupdata2 groupdata2 Public

    R-package: Methods for dividing data into groups. Create balanced partitions and cross-validation folds. Perform time series windowing and general grouping and splitting of data. Balance existing g…

    R 27 3

  2. cvms cvms Public

    R Package: Cross-validate one or multiple gaussian or binomial regression models at once. Perform repeated cross-validation. Returns results in a tibble for easy comparison, reporting and further a…

    R 39 7

  3. xpectr xpectr Public

    R package for generating expectations for `testthat` unit testing

    R 37 1

  4. rearrr rearrr Public

    Rearrrange data by a set of methods

    R 24 3

  5. nattrs nattrs Public

    Nested attributes/dict members utility functions for python.

    Python 1

  6. utipy utipy Public

    Python utilities, e.g. for pandas

    Python 2

0