Repositories list

• EEB384K-workshops

  Public
  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Oct 14, 2025Oct 14, 2025

• AI-models

  Public
  Tools and documentation for running various AI models

  Jupyter Notebook

  •0•2•0•0•Updated Oct 3, 2025Oct 3, 2025

• wilkelab.github.io

  Public
  HTML

  •3•2•0•0•Updated Sep 23, 2025Sep 23, 2025

• gridtext

  Public
  Improved text rendering support for grid graphics in R

  R

  •

  Other

  •19•97•17•4•Updated Sep 19, 2025Sep 19, 2025

• ggridges

  Public
  Ridgeline plots in ggplot2

  R

  •

  GNU General Public License v2.0

  •33•422•44•3•Updated Aug 27, 2025Aug 27, 2025

• DSC385

  Public
  JavaScript

  •

  MIT License

  •0•0•0•0•Updated Jul 21, 2025Jul 21, 2025

• cowplot

  Public
  cowplot: Streamlined Plot Theme and Plot Annotations for ggplot2

  R

  •84•742•34•2•Updated Jul 7, 2025Jul 7, 2025

• SDS366

  Public
  SDS 366 Data Visualization

  JavaScript

  •

  MIT License

  •5•13•0•0•Updated Jul 3, 2025Jul 3, 2025

• ungeviz

  Public
  Tools for visualizing uncertainty with ggplot2

  R

  •9•157•5•0•Updated Mar 6, 2025Mar 6, 2025

• dataviz_shortcourse

  Public
  Materials for a dataviz shortcourse

  HTML

  •

  MIT License

  •1•7•0•0•Updated Aug 11, 2024Aug 11, 2024

• SDS375

  Public
  SDS 375 Data Visualization in R

  HTML

  •87•288•1•0•Updated Apr 24, 2024Apr 24, 2024

• cinful

  Public
  A fully automated pipeline to identify microcins along with their associated immunity proteins and export machinery

  Pep8

  •

  GNU General Public License v3.0

  •1•7•3•0•Updated Apr 11, 2024Apr 11, 2024

• DSC385_old

  Public
  HTML

  •

  MIT License

  •9•16•1•1•Updated Apr 2, 2024Apr 2, 2024

• ggtext

  Public
  Improved text rendering support for ggplot2

  R

  •

  GNU General Public License v2.0

  •37•665•45•2•Updated Dec 19, 2023Dec 19, 2023

• sicegar

  Public
  R package for the analysis of single cell virology growth curves

  R

  •9•9•3•1•Updated Jan 31, 2023Jan 31, 2023

• cinful_data_analysis

  Public
  A repository for the analysis involved in "Evidence for widespread class II microcins in Enterobacterales genomes"

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•3•0•0•Updated Oct 19, 2022Oct 19, 2022

• ggplot2_archive

  Public
  An implementation of the Grammar of Graphics in R

  R

  •

  Other

  •2.1k•2•0•0•Updated Jul 7, 2022Jul 7, 2022

• Opfi

  Public
  A Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets.

  Python

  •

  MIT License

  •5•21•3•0•Updated Oct 26, 2021Oct 26, 2021

• Metagenomics_CAST

  Public
  Metagenomic search for novel CRISPR-transposons

  C++

  •5•12•1•0•Updated Sep 30, 2021Sep 30, 2021

• CRISPR_associated_transposons

  Public
  0•0•0•0•Updated Aug 17, 2021Aug 17, 2021

• practicalgg

  Public
  Practical ggplot2

  R

  •

  Other

  •6•74•1•0•Updated Feb 1, 2021Feb 1, 2021

• wilkelab.github.io.archive_sep_2020

  Public
  Source for wilkelab.org website

  HTML

  •3•7•0•0•Updated Sep 5, 2020Sep 5, 2020

• glhlth590

  Public
  CSS

  •0•0•0•0•Updated Apr 26, 2020Apr 26, 2020

• rates_measurement

  Public
  Shell

  •2•0•0•0•Updated Sep 11, 2018Sep 11, 2018

• r4s_benchmark

  Public
  Shell

  •0•3•0•0•Updated Sep 6, 2018Sep 6, 2018

• influenza_codon_usage

  Public
  Data and code for Smith et al., Avian Influenza Virus PB1 Gene in H3N2 Viruses Evolved in Humans To Reduce Interferon Inhibition by Skewing Codon Usage toward Interferon-Altered tRNA Pools, mBio 2018

  Python

  •1•1•0•0•Updated Jun 28, 2018Jun 28, 2018

• eGFP_deletion_prediction

  Public
  R

  •0•1•0•0•Updated Feb 26, 2017Feb 26, 2017

• Ecoli_PTMs

  Public
  Code and data for Brown et al., Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions

  Jupyter Notebook

  •2•1•0•0•Updated Aug 30, 2016Aug 30, 2016

• influenza_H3N2_passaging

  Public
  Data and code for McWhite et al., Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin, Virus Evolution (2016)

  HyPhy

  •2•2•0•0•Updated Aug 24, 2016Aug 24, 2016

• ProteinEvolutionToolbox

  Public
  Python

  •8•15•0•0•Updated Mar 25, 2016Mar 25, 2016