jrherr

2014-04-29-gwu

Software Carpentry Bootcamp at George Washington University on April 29th-30th 2014

2015-01-27-msu_icer

Software Carpentry Bootcamp held at Michigan State University on January 27th to 29th, 2015

oneliners

Useful bash one-liners for bioinformatics.

2014-06-26-nd

Software Carpentry Bootcamp on June 26th-27th, 2014, at Notre Dame University

2014-07-10-esip

Software Carpentry Bootcamp on July 10th-11th, 2014, at ESIP meeting in Frisco, CO, USA

2014-07-24-beacon

Data Carpentry workshop July 24-25 BEACON

2014-09-11-udel

Software Carpentry Bootcamp on September 11th-12th, 2014, at the University of Delaware

cheat_sheets

Chicken

This is the chicken paper repositiory

cloaked-octo-wallhack

This is Josh's working folder for daily progress reports

ConditionallyRareTaxa

R scripts and tutorial datasets to detect conditionally rare taxa in time series of microbial communities

datacarpentry

Data Carpentry workshop materials

datacarpentry.github.io

Website for data carpentry

gam-ngs

Genomic Assemblies Merger for NGS

khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

knowyourdata-genomics

Lesson on Getting to Know Your Data for genomics

makefile-example

An example of a data analysis pipeline using Make

meteor-gazelle

A framework built using Meteor.

mlst

Scan contig files against PubMLST typing schemes

mothur_ami

Repository to create and maintain an Amazon AMI for mothur

nanopore-scripts

Various scripts and recipes for working with nanopore data

notebook

Open Lab Notebook

POPBAM

POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments

q2oligo

Convert QIIME files into Oligotyping subsets.

qiime

Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests

refweak

A list of weak Bacterial assemblies in GenBank

reviews

Writing reviews of academic papers

rusda

Interface to USDA Databases

site

Software Carpentry web site.

sql-ecology

Lesson on using the SQL for ecology