jrherr/2014-04-29-gwu
Software Carpentry Bootcamp at George Washington University on April 29th-30th 2014
Developer Profile
jrherr
Discovered public repositories for jrherr in the GitHub catalog.
jrherr/Punchcard
Generate GitHub-style punchcard charts with ease.
jrherr/jmpress.js
A jQuery plugin to build a website on the infinite canvas
jrherr/httr
httr: a friendly http package for R
jrherr/Rphylip
An R interface for PHYLIP.
jrherr/Rforecastio
Simple R interface to forecast.io weather data
jrherr/vectoreditor
Web based DNA sequence editing and analysis tool
jrherr/bioinformatics
Tools for bioinformatics
jrherr/SimSeq
An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.
jrherr/BugBuilder
Hands-free microbial genome assembly
jrherr/R-GIS-tutorial
Spatial data in R: using R as a GIS
jrherr/2014-03-17-purdue
Bootcamp at Purdue University in March 2014
jrherr/CONTIGuator
Bacterial genomes finishing tool for structural insights on draft genomes
jrherr/bioinformatics_scripts
Just a bunch of scripts I use for bioinformatics -- feel free to use, reuse, and improve
jrherr/startbootstrap
Better HTML Starter Templates for Bootstrap 3
jrherr/sff2fastq
extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output
jrherr/bedtools2
A powerful toolset for genome arithmetic.
jrherr/samtools
This is the official development repository for samtools.
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/metAMOS
A metagenomic and isolate genome assembly pipeline built with AMOS
jrherr/jekyll-lunr-js-search
Jekyll + lunr.js = static websites with powerful full-text search using JavaScript
jrherr/homebrew-cask
a friendly homebrew-style CLI workflow for the administration of Mac applications distributed as binaries
jrherr/Sibelia
Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.
jrherr/jbrowse
A modern genome browser built with JavaScript and HTML5.
jrherr/blacktie
Blacktie: a streamlined interface to the popular tophat/cufflinks RNA-seq pipeline
jrherr/velour
memory efficient short read de novo DNA sequence assembly tool for gigabase genomes
jrherr/poppin
A tool for bacterial gene assembly.
jrherr/homebrew-science
Scientific formulae for the Homebrew package manager
jrherr/jekyll-bootstrap
The quickest way to start and publish your Jekyll powered blog. 100% compatible with GitHub pages.
jrherr/jrherr.github.com
Open Notebook
jrherr/seqtk
Toolkit for processing sequences in FASTA/Q formats
jrherr/solarplot
Mitochondrial Solar Plot
jrherr/d3
A JavaScript visualization library for HTML and SVG.
jrherr/wgsim
Reads simulator
jrherr/webgl-globe
WebGL Globe is a platform for visualizing latitude longitude based information using WebGL.
jrherr/Topiary-Explorer
Interactive phylogenetic tree viewing software
jrherr/WiggleTools
Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency
jrherr/illumina-utils
A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
jrherr/EMIRGE
EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
jrherr/taxize
Search web taxonomy sites and download data
jrherr/oneliners
Useful bash one-liners for bioinformatics.
jrherr/2014-01-27-indiana
Bootcamp at Indiana University Jan 2014
jrherr/its-reference-otus
A reference set of ITS OTUs derived from UNITE for use with QIIME
jrherr/American-Gut
American Gut open-access data and IPython notebooks
jrherr/libcrispr
A small library for dealing with .crispr files
jrherr/oligotyping
Exploring microbial patterns through subtle nucleotide variation within 16S rRNA gene tag sequences of closely related taxa
jrherr/trimal
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 1.4
jrherr/readUntangler
Public repository.
jrherr/crisprtools
small utilities for manipulating .crispr files
jrherr/crass
The CRISPR assembler