jrherr

quick_basic_R_tutorial

This is a quick and basic tutorial for R

2014-01-27-indiana

Bootcamp at Indiana University Jan 2014

American-Gut

American Gut open-access data and IPython notebooks

ascii_plots

Convenience function for quick and dirty data analysis

bio-info-hack

Research code for various bioinformatics projects

BugBuilder

Hands-free microbial genome assembly

crass

The CRISPR assembler

crisprtools

small utilities for manipulating .crispr files

EMIRGE

EMIRGE reconstructs full length ribosomal genes from short read sequencing data.

ggplot-lecture

My lecture on ggplot at Cal (spring 2013)

illumina-utils

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).

impress.js

It's a presentation framework based on the power of CSS3 transforms and transitions in modern browsers and inspired by the idea behind prezi.com.

jekyll-lunr-js-search

Jekyll + lunr.js = static websites with powerful full-text search using JavaScript

migaap

My Working Microbial Genome Assembly & Annotation Pipeline

minced

Mining CRISPRs in Environmental Datasets

MIX

MIX: Combining multiple assemblies from NGS data

oligotyping

Exploring microbial patterns through subtle nucleotide variation within 16S rRNA gene tag sequences of closely related taxa

pyBWA

Python libraries to interact with BWA mapper

R-GIS-tutorial

Spatial data in R: using R as a GIS

readUntangler

Rforecastio

Simple R interface to forecast.io weather data

sabre

seqtk

Toolkit for processing sequences in FASTA/Q formats

sff2fastq

extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output

solarplot

Mitochondrial Solar Plot

srst2

Short Read Sequence Typing for Bacterial Pathogens

trimal

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 1.4

velour

memory efficient short read de novo DNA sequence assembly tool for gigabase genomes

webgl-globe

WebGL Globe is a platform for visualizing latitude longitude based information using WebGL.

WiggleTools

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency