wilkelab/ProteinEvolutionToolbox

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14
Rank 1,390,558 (Top 29 %)
Language
Python
Created almost 11 years ago
Updated about 8 years ago

wilkelab/ProteinEvolutionToolbox

wilkelab

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cowplot

cowplot: Streamlined Plot Theme and Plot Annotations for ggplot2

ggtext

Improved text rendering support for ggplot2

ggridges

Ridgeline plots in ggplot2

SDS375

SDS 375 Data Visualization in R

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

Metagenomics_CAST

Metagenomic search for novel CRISPR-transposons

influenza_HA_evolution

sicegar

R package for the analysis of single cell virology growth curves

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

r4s_benchmark

EBOV_H1N1

cinful_data_analysis

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

Jupyter Notebook

wilkelab.github.io

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)

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.