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/quick_basic_R_tutorial
This is a quick and basic tutorial for R
jrherr/2014-01-27-indiana
Bootcamp at Indiana University Jan 2014
jrherr/American-Gut
American Gut open-access data and IPython notebooks
jrherr/ascii_plots
Convenience function for quick and dirty data analysis
jrherr/bio-info-hack
Research code for various bioinformatics projects
jrherr/BugBuilder
Hands-free microbial genome assembly
jrherr/crass
The CRISPR assembler
jrherr/crisprtools
small utilities for manipulating .crispr files
jrherr/EMIRGE
EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
jrherr/ggplot-lecture
My lecture on ggplot at Cal (spring 2013)
jrherr/illumina-utils
A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
jrherr/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.
jrherr/jekyll-lunr-js-search
Jekyll + lunr.js = static websites with powerful full-text search using JavaScript
jrherr/migaap
My Working Microbial Genome Assembly & Annotation Pipeline
jrherr/minced
Mining CRISPRs in Environmental Datasets
jrherr/MIX
MIX: Combining multiple assemblies from NGS data
jrherr/oligotyping
Exploring microbial patterns through subtle nucleotide variation within 16S rRNA gene tag sequences of closely related taxa
jrherr/pyBWA
Python libraries to interact with BWA mapper
jrherr/R-GIS-tutorial
Spatial data in R: using R as a GIS
jrherr/readUntangler
jrherr/Rforecastio
Simple R interface to forecast.io weather data
jrherr/sabre
jrherr/seqtk
Toolkit for processing sequences in FASTA/Q formats
jrherr/sff2fastq
extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output
jrherr/solarplot
Mitochondrial Solar Plot
jrherr/srst2
Short Read Sequence Typing for Bacterial Pathogens
jrherr/trimal
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 1.4
jrherr/velour
memory efficient short read de novo DNA sequence assembly tool for gigabase genomes
jrherr/webgl-globe
WebGL Globe is a platform for visualizing latitude longitude based information using WebGL.
jrherr/WiggleTools
Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency