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GRIDSS: the Genomic Rearrangement IDentification Software Suite
Functional highly reproducible bioinformatics pipelines
R package designed to simplify structural variant analysis
PathOS is a clinical application for filtering, analysing and reporting on NGS variants
Data, metadata and analyses performed in microbiome 16s rRNA amplicon sequencing data and whole metagenomics sequencing data of women with and without T1D during pregnancy.
Short pieces of useful code
Analysis pipeline for CASCADE data
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.
Anomaly annotation web service
Bioinformatics pipelines with Haskell and Shake
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
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