Pinned Repositories
ngseasy
Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
awesome-genetics-software
A list of cool software for genetic analysis and the like
BRC_MH_Bioinformatics
Collection of pipelines, workflows and scripts for processing SNP and gene expression arrays and NGS data
broom
Convert statistical analysis objects from R into tidy format
datasharing
The Leek group guide to data sharing
enrichr-api
python script to programmatically enrich your data using Enrichr API
exotic-dna-ngs
WIP & POC: Count Viral and other non-human genome signatures in Human NGS data
ml_h2o_spark
playing with Sparkling Water
TextHunter
TextHunter - User Friendly Annotation and Concept Extraction Tool
snewhouse's Repositories
snewhouse/broom
Convert statistical analysis objects from R into tidy format
snewhouse/docker-cheat-sheet
Docker Cheat Sheet
snewhouse/docker-squash
Squash docker images to make them smaller
snewhouse/advanced-redcap-interfaces
A talk concerning advanced REDCap interfaces and how they can help to improve research.
snewhouse/bcbio-nextgen
Validated, scalable, community developed variant calling and RNA-seq analysis
snewhouse/bcbio.variation
Toolkit to analyze genomic variation data, built on the GATK with Clojure
snewhouse/biobambam
Tools for bam file processing
snewhouse/brc-bioinformatics-eccb-2014
Abstracts presented at ECCB 2014
snewhouse/courses
Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1
snewhouse/data-science-at-the-command-line
Data Science at the Command Line
snewhouse/datasciencecoursera
sjn data science coursera
snewhouse/docker
A collection of docker recipes
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/ensembl-tools
Ensembl tools including the VEP
snewhouse/freebayes
Bayesian haplotype-based polymorphism discovery and genotyping.
snewhouse/homebrew
The missing package manager for OS X.
snewhouse/IGV
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
snewhouse/ipython-notebook
Docker container for the IPython notebook
snewhouse/juice-shop
An intentionally insecure RIA suitable for pen testing and security awareness trainings written in Node, Express and Angular.
snewhouse/npg_docker
Summer Placement Project @ Wellcome Trust Sanger Instute, Hinxton
snewhouse/open-vagrant-boxes
Docker-compatible Vagrant base boxes
snewhouse/picard
A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.
snewhouse/pipework
Software-Defined Networking tools for LXC (LinuX Containers)
snewhouse/rocker
R configurations for Docker
snewhouse/rocker-paper
snewhouse/sga
de novo sequence assembler using string graphs
snewhouse/sga-extra
Extra tools and utilities for sga
snewhouse/shinyapps
Deploy Shiny applications to ShinyApps
snewhouse/vagrant
Vagrant is a tool for building and distributing development environments.
snewhouse/varcmp