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ag3c_starvation_tc_rnaseq

RNA-seq pipeline for E. coli starvation time course

cinful

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

cinful_data_analysis

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

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

cowplot: Streamlined Plot Theme and Plot Annotations for ggplot2

crispr_associated_transposons

dataviz_shortcourse

Materials for a dataviz shortcourse

dsc385

ebov_h1n1

ecoli_ptms

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

egfp_deletion_prediction

ggplot2_archive

An implementation of the Grammar of Graphics in R

ggridges

Ridgeline plots in ggplot2

ggtext

Improved text rendering support for ggplot2

glhlth590

gridtext

Improved text rendering support for grid graphics in R

hiv_ranbp2_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

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)

influenza_ha_evolution

influenza_ph1n1_timecourse

macv_tfr1_modeling

metagenomics_cast

Metagenomic search for novel CRISPR-transposons

opfi

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

practicalgg

Practical ggplot2

proteinevolutiontoolbox

r4s_benchmark

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.

rates_measurement

sds375

SDS 375 Data Visualization in R