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A simple web page that uses the Google maps API to track time spent in traffic
Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
Multiple Whole Genome Alignment Testing Suite
Code, docs and experiments for the MSCA project.
quick_plot is a python program that plots one or two column flat files from the command line.
Script to plot 1D data in 2D using the Hilbert Curve. Honestly a pretty terrible visualization technique for conveying information, but it looks cool.
Tools to create plots showing N-statistics for genome assemblies
The R function stem() ported to run on the command line for use in pipes!
Structure Harvester is a program for parsing the output of Pritchard's STRUCTURE and for performing the Evanno method.
CVE-2014-0160 mass scan on the Alexa top sites.
Analysis scripts to generate Tables and Figures for Assemblathon 1
cairo_visualization_wheel is a Python script that uses matplotlib to create visualization wheels as seen in Alberto Cairo's book The Functional Art http://www.thefunctionalart.com/2012/09/download-three-chapters-of-functional.html (see Figure 3.2).
Script to handle superscripted numbers for academic papers that have many authors (>20) and complex affiliations
summary() from the R project refactored to run on the command line for use in pipes!
Convenience function for quick and dirty data analysis
Given a multiple sequence alignment and a phylogeny relating the aligned sequences, StatSigMAw assesses every site of the alignment and identifies suspiciously aligned regions in the alignment. Xiaoyu Chen and Martin Tompa, "Comparative assessment of methods for aligning multiple genome sequences". Nature Biotechnology, vol. 28, no. 6, June 2010…
Utility to mask fasta formated files using a .bed file to define the regions to mask.
Signaling Pathway Impact Analysis (SPIA) refactored into C
jobTree based python wrapper to run the genome simulation tool suite Evolver
Scripts and Makefile to generate infile set for the Evolver suite of genome evolution simulation tools.
mafJoin is a tool for combining pairs of MAF files that share a common sequence.
A script to make Fisher-Wright Coalescent plots using dot from graphviz