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Wilke Lab's Projects

cinful icon cinful

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

cinful_data_analysis icon cinful_data_analysis

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

complex_divergence_simul icon 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

cowplot icon cowplot

cowplot: Streamlined Plot Theme and Plot Annotations for ggplot2

ecoli_ptms icon ecoli_ptms

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

ggtext icon ggtext

Improved text rendering support for ggplot2

gridtext icon gridtext

Improved text rendering support for grid graphics in R

influenza_codon_usage icon 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

influenza_h3n2_passaging icon 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)

opfi icon opfi

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

rate_variability_variation icon 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.

sds375 icon sds375

SDS 375 Data Visualization in R

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