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Functional highly reproducible bioinformatics pipelines
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Bioinformatics pipelines with Haskell and Shake
R package designed to simplify structural variant analysis
Short pieces of useful code
Comprehensive benchmark of structural variant callers
Web-based copy number browser.
A pipeline for the assembly of VAR genes from transcriptome data
classification of higher-order structural variants from breakpoint data
PathOS is a decision support tool for NGS variants
By modelling aneuploidy with interleaving branching processes we can make a decision about whether or not genome doubling occurred. We can also label each event as being pre or post GD.
Extracts copy number estimates from NGS data.
A fast and self-contained amplicon pipeline tool.
Tools used to apply QDNASeq R package to our P. falciparum data, including forging a BSGenome package
Code for ENDIA microbiome QC paper
Structural Variation Quality Score Calculator
A few tools for plotting and reasoning about genomic structural variants.
Python library for munging biological sequence and annotation data
allocates NGS reads to VAR domain models
This project contains simple methods to measure sample relatedness and identify potential swaps and contamination
MHC Class I Gene Search tool
Short read tools - a small python package with some convenience modules for dealing with short read data