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alderman-vote-tracker

Board of Alderman Vote Tracker for City of St. Louis

all1_panel_plots

A series of scripts to make panel plots for CNVs and regions of LOH across the genome.

arnav

Mutation calling using a site-specific binomial model

avi-phd-thesis

My PhD dissertation at Washington University in St. Louis

bam-parser-tutorial

A simple example of parsing BAM files using htslib

breakdancer

SV detection from paired end reads mapping

castools

Command line tool for the CAS project

civic-api-client

Example tools using the CIVIC API

common_scripts_gblab

DEPRECATED

cse232

Course notes for CSE 232 at Washington University

csg-project

Comp stat gen project

datasets

A collection of awesome data sets to practice various kinds of analyses.

denovogear

A program to detect denovo-variants using next-generation sequencing data. (http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html)

denovogear-bb

denovo caller using beta binomial likelihoods

denovogear-legacy

Statistical model to detect de-novo mutations using sequencing data from trios and pairs.

denovogear-vntr-code

denovogear-VNTR-code

dng_betabinomial_paired

DeNovoGear with BetaBinomial likelihoods for paired sample mutation calling. For example this package can be used to do tumor vs normal comparisons. The BetaBinomial likelihood model has been shown to have a higher sensitivity and specificity compared to the binomial model.

duc-newspaper-analysis

Newspaper analysis

fdr

Control the false discovery rate using the Benjamini Hochberg procedure in C++

fisher-exact

The fisher exact test from htslib

gatoradd

genome

genome-db-tgi-cancer-annotation-data

Unofficial repo for software vendoring or packaging purposes

genomics

genomics assignments

genomicsspring2017

genvisr

Genome data visualizations

gms

The Genome Modeling System installer (BETA).

guesswho

gzip_reader

An example for reading gzipped files in C++

hedgehog-variability

Notebooks and code used for the hedgehog variability project