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cowplotcowplot: Streamlined Plot Theme and Plot Annotations for ggplot2
ggtextImproved text rendering support for ggplot2
ggridgesRidgeline plots in ggplot2
SDS375SDS 375 Data Visualization in R
ungevizTools for visualizing uncertainty with ggplot2
OpfiA Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets.
Metagenomics_CASTMetagenomic search for novel CRISPR-transposons
sicegarR package for the analysis of single cell virology growth curves
wilkelab.github.io.archive_sep_2020Source for wilkelab.org website
cinfulA fully automated pipeline to identify microcins along with their associated immunity proteins and export machinery
dataviz_shortcourseMaterials for a dataviz shortcourse
cinful_data_analysisA repository for the analysis involved in "Evidence for widespread class II microcins in Enterobacterales genomes"
influenza_H3N2_passagingData 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)
complex_divergence_simulCode 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
rate_variability_variationCode 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.
influenza_codon_usageData 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_variationCode and data for Echave et al., Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites, Phys. Biol. 12:025002, 2015.