Pinned Repositories
breaksembler
cloudbreak
The Cloudbreak Hadoop-based Genomic Structural Variation Caller
cnv-validation
defense
permuting-feature-enrichment-test
A tool to test the enrichment of genomic features by permutations
project_scripts
Scripts for various projects
sv-annotate
A small pipeline to annotate and filter candidate structural variation calls
svfactorie
Detect genomic structural variations using conditional random fields in the Factorie framework
svpipeline
cwhelan's Repositories
cwhelan/cloudbreak
The Cloudbreak Hadoop-based Genomic Structural Variation Caller
cwhelan/sv-annotate
A small pipeline to annotate and filter candidate structural variation calls
cwhelan/permuting-feature-enrichment-test
A tool to test the enrichment of genomic features by permutations
cwhelan/project_scripts
Scripts for various projects
cwhelan/svfactorie
Detect genomic structural variations using conditional random fields in the Factorie framework
cwhelan/svpipeline
cwhelan/breaksembler
cwhelan/cnv-validation
cwhelan/defense
cwhelan/gatk-linked-reads
Official code repository for GATK versions 4 and up
cwhelan/htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
cwhelan/jclouds
jclouds is an open source library that helps you get started in the cloud and reuse your java development skills. Our api allows you to freedom to use portable abstractions or cloud-specific features. We support many clouds including Amazon, VMWare, Azure, and Rackspace.
cwhelan/mocha
MOsaic CHromosomal Alterations (MoChA) caller
cwhelan/quartetibdanalysis
Tools for analyzing IBD state and copy number variation in quartet sequencing experiments
cwhelan/shapeit4
Segmented HAPlotype Estimation and Imputation Tool
cwhelan/TAG-public
Official workflows published by the Broad Institute's Genomics Platform Translation Analysis Group (TAG)
cwhelan/thesis
cwhelan/variant-interpretation
cwhelan/warp
WDL Analysis Research Pipelines