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Dent Earl's Projects

ascii_plots icon ascii_plots

Convenience function for quick and dirty data analysis

authoraffiliations icon authoraffiliations

Script to handle superscripted numbers for academic papers that have many authors (>20) and complex affiliations

avgviewer icon avgviewer

Ancestral Variation Graph (AVG) viewer in javascript

cairo_visualization_wheel icon cairo_visualization_wheel

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).

evolverinfilegeneration icon evolverinfilegeneration

Scripts and Makefile to generate infile set for the Evolver suite of genome evolution simulation tools.

evolversimcontrol icon evolversimcontrol

jobTree based python wrapper to run the genome simulation tool suite Evolver

famask icon famask

Utility to mask fasta formated files using a .bed file to define the regions to mask.

mafjoin icon mafjoin

mafJoin is a tool for combining pairs of MAF files that share a common sequence.

maftools icon maftools

Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.

quick_plot icon quick_plot

quick_plot is a python program that plots one or two column flat files from the command line.

simplehilbertcurve icon simplehilbertcurve

Script to plot 1D data in 2D using the Hilbert Curve. Honestly a pretty terrible visualization technique for conveying information, but it looks cool.

spia_c icon spia_c

Signaling Pathway Impact Analysis (SPIA) refactored into C

statsigma-w icon statsigma-w

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, 567-572. doi:10.1038/nbt.1637

stem icon stem

The R function stem() ported to run on the command line for use in pipes!

structureharvester icon structureharvester

Structure Harvester is a program for parsing the output of Pritchard's STRUCTURE and for performing the Evanno method.

summary icon summary

summary() from the R project refactored to run on the command line for use in pipes!

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