wilkelab/SDS375

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wilkelab/SDS375

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SDS 375 Data Visualization in R

SDS 375: Data Visualization in R

This repository holds the source materials used to create the class site available at: https://wilkelab.org/SDS375

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Any computer code (R, HTML, CSS, etc.) in slides and worksheets, including in slide and worksheet sources, is also licensed under MIT.

cowplot

cowplot: Streamlined Plot Theme and Plot Annotations for ggplot2

ggtext

Improved text rendering support for ggplot2

ggridges

Ridgeline plots in ggplot2

ungeviz

Tools for visualizing uncertainty with ggplot2

gridtext

Improved text rendering support for grid graphics in R

practicalgg

Practical ggplot2

Opfi

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

DSC385

ProteinEvolutionToolbox

Metagenomics_CAST

Metagenomic search for novel CRISPR-transposons

sicegar

R package for the analysis of single cell virology growth curves

influenza_HA_evolution

wilkelab.github.io.archive_sep_2020

Source for wilkelab.org website

cinful

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

influenza_pH1N1_timecourse

dataviz_shortcourse

Materials for a dataviz shortcourse

EBOV_H1N1

r4s_benchmark

cinful_data_analysis

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

Jupyter Notebook

influenza_H3N2_passaging

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)

wilkelab.github.io

complex_divergence_simul

Code and data for PPI simulation part of Kachroo et al., Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science 348:921–925, 2015

eGFP_deletion_prediction

rate_variability_variation

Code and data for Jackson et al., Intermediate divergence levels maximize the strength of structure–sequence correlations in enzymes and viral proteins, Protein Science, in press.

MACV_TfR1_modeling

influenza_codon_usage

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

therm_constraints_rate_variation

Code and data for Echave et al., Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites, Phys. Biol. 12:025002, 2015.