snewhouse/glu-genetics
Automatically exported from code.google.com/p/glu-genetics
Developer Profile
snewhouse
Discovered public repositories for snewhouse in the GitHub catalog.
snewhouse/rocker-paper
Public repository.
snewhouse/gitignore
A collection of useful .gitignore templates
snewhouse/alignment-and-variant-calling-tutorial
basic walk-throughs for alignment and variant calling from NGS sequencing data
snewhouse/courses
Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1
snewhouse/sci
Gentoo Science Overlay
snewhouse/ad_brain_expression
ad brain expression analyses of public data
snewhouse/genome-data-integration
Methods to integrate data from multiple genome sequencing datasets and form consensus variant calls
snewhouse/sga-extra
Extra tools and utilities for sga
snewhouse/datasharing
The Leek group guide to data sharing
snewhouse/datasciencecoursera
sjn data science coursera
snewhouse/data-science-at-the-command-line
Data Science at the Command Line
snewhouse/docker-speedseq
Dockerfile for speedseq
snewhouse/rocker
R configurations for Docker
snewhouse/biobambam
Tools for bam file processing
snewhouse/bcbio.variation
Toolkit to analyze genomic variation data, built on the GATK with Clojure
snewhouse/juice-shop
An intentionally insecure RIA suitable for pen testing and security awareness trainings written in Node, Express and Angular.
snewhouse/ipython-notebook
Docker container for the IPython notebook
snewhouse/docker-desktop
Docker Desktop enables you to create virtual desktops that can be accessed remotely. It comes with Firefox and Libreoffice already installed!
snewhouse/npg_docker
Summer Placement Project @ Wellcome Trust Sanger Instute, Hinxton
snewhouse/shiny_example
Example shiny app
snewhouse/vagrant
Vagrant is a tool for building and distributing development environments.
snewhouse/homebrew
The missing package manager for OS X.
snewhouse/open-vagrant-boxes
Docker-compatible Vagrant base boxes
snewhouse/dvm
An on demand Docker virtual machine, thanks to Vagrant and boot2docker. Works great on Macs and other platforms that don't natively support the Docker daemon. Support VirtualBox, VMware, and Parallels.
snewhouse/docker-cheat-sheet
Docker Cheat Sheet
snewhouse/broom
Convert statistical analysis objects from R into tidy format
snewhouse/pipework
Software-Defined Networking tools for LXC (LinuX Containers)
snewhouse/freebayes
Bayesian haplotype-based polymorphism discovery and genotyping.
snewhouse/picard
A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.
snewhouse/brc-bioinformatics-eccb-2014
Abstracts presented at ECCB 2014
snewhouse/docker-squash
Squash docker images to make them smaller
snewhouse/sga
de novo sequence assembler using string graphs
snewhouse/fermi
A WGS de novo assembler based on the FMD-index for large genomes
snewhouse/varcmp
Public repository.
snewhouse/bioawk
BWK awk modified for biological data
snewhouse/IGV
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
snewhouse/blacktie
Blacktie: a streamlined interface to the popular tophat/cufflinks RNA-seq pipeline
snewhouse/ensembl-tools
Ensembl tools including the VEP
snewhouse/mutect
MuTect -- Accurate and sensitive cancer mutation detection
snewhouse/ngs
Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
snewhouse/fastx_toolkit
FASTA/FASTQ pre-processing programs
snewhouse/fastq-tools
Small utilities for working with fastq sequence files.
snewhouse/bcbio-nextgen
Validated, scalable, community developed variant calling and RNA-seq analysis
snewhouse/shinyapps
Deploy Shiny applications to ShinyApps
snewhouse/l1ktools
Public repository.
snewhouse/TextHunter
TextHunter - User Friendly Annotation and Concept Extraction Tool
snewhouse/seqtk
Toolkit for processing sequences in FASTA/Q formats
snewhouse/delly
DELLY: Structural variant discovery by integrated paired-end and split-read analysis
snewhouse/Biostat-578
A repository for all of my teaching material