dentearl/stem

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Language
C
License
GNU General Publi...
Created over 13 years ago
Updated about 10 years ago

dentearl/stem

dentearl

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

mafTools

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

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.

structureHarvester

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

quick_plot

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

evolverSimControl

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

assemblAnalysis

Analysis scripts to generate Tables and Figures for Assemblathon 1

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).

n50PlottingTools

Tools to create plots showing N-statistics for genome assemblies

summary

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

authorAffiliations

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

mwgAlignAnalysis

Multiple Whole Genome Alignment Testing Suite

avgViewer

Ancestral Variation Graph (AVG) viewer in javascript

mafJoin

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

fisherWrightCoalPlotter

A script to make Fisher-Wright Coalescent plots using dot from graphviz

spia_c

Signaling Pathway Impact Analysis (SPIA) refactored into C

evolverInfileGeneration

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

faMask

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

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