jrherr
I am an Assistant Professor at the University of Nebraska. I study the genomics and metagenomics of plant-microbe interactions with a focus on mycology.
University of NebraskaLincoln, NE, USA
Pinned Repositories
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
alignerviz
A simple tool to visualize sequences using Vlachos et al's technique
bioinformatics_scripts
Just a bunch of scripts I use for bioinformatics -- feel free to use, reuse, and improve
fasta_utilities
A collection of scripts developed to interact with fasta, fastq and sam/bam files.
ggplot2-tutorial
Teaching materials for the R package ggplot2
jrherr.github.com
Open Notebook
oneliners
Useful bash one-liners for bioinformatics.
quick_basic_R_tutorial
This is a quick and basic tutorial for R
jrherr's Repositories
jrherr/2014-04-29-gwu
Software Carpentry Bootcamp at George Washington University on April 29th-30th 2014
jrherr/2015-01-27-msu_icer
Software Carpentry Bootcamp held at Michigan State University on January 27th to 29th, 2015
jrherr/oneliners
Useful bash one-liners for bioinformatics.
jrherr/2014-06-26-nd
Software Carpentry Bootcamp on June 26th-27th, 2014, at Notre Dame University
jrherr/2014-07-10-esip
Software Carpentry Bootcamp on July 10th-11th, 2014, at ESIP meeting in Frisco, CO, USA
jrherr/2014-07-24-beacon
Data Carpentry workshop July 24-25 BEACON
jrherr/2014-09-11-udel
Software Carpentry Bootcamp on September 11th-12th, 2014, at the University of Delaware
jrherr/cheat_sheets
jrherr/Chicken
This is the chicken paper repositiory
jrherr/cloaked-octo-wallhack
This is Josh's working folder for daily progress reports
jrherr/ConditionallyRareTaxa
R scripts and tutorial datasets to detect conditionally rare taxa in time series of microbial communities
jrherr/datacarpentry
Data Carpentry workshop materials
jrherr/datacarpentry.github.io
Website for data carpentry
jrherr/gam-ngs
Genomic Assemblies Merger for NGS
jrherr/khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
jrherr/knowyourdata-genomics
Lesson on Getting to Know Your Data for genomics
jrherr/makefile-example
An example of a data analysis pipeline using Make
jrherr/meteor-gazelle
A framework built using Meteor.
jrherr/mlst
Scan contig files against PubMLST typing schemes
jrherr/mothur_ami
Repository to create and maintain an Amazon AMI for mothur
jrherr/nanopore-scripts
Various scripts and recipes for working with nanopore data
jrherr/notebook
Open Lab Notebook
jrherr/POPBAM
POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments
jrherr/q2oligo
Convert QIIME files into Oligotyping subsets.
jrherr/qiime
Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests
jrherr/refweak
A list of weak Bacterial assemblies in GenBank
jrherr/reviews
Writing reviews of academic papers
jrherr/rusda
Interface to USDA Databases
jrherr/site
Software Carpentry web site.
jrherr/sql-ecology
Lesson on using the SQL for ecology