Pinned Repositories
AlphaThal
Pipeline for retrieving reads from the Alpha Thalassemia region
bam2mpg
Software for calling variants from next-generation sequence data.
BardCNV
BardCNV calls copy number variants from next generation sequencing data.
mlgenofeatures
mlgenotype
Python package for training and using machine learning models to recognize structural variants using features of aligned short read data
MMBVariantCalling
Scripts and updates for running the variant pipeline described in "Variant Calling From Next Generation Sequence Data" by Nancy F. Hansen
NovoGraph
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
q100bench
Software for comparing genome assemblies and read datasets to a benchmark genome like the Q100 project's HG002v1.0.1
Shimmer
Shimmer is a software package for the characterization of genetic differences between two very similar samples, e.g., a tumor sample and its matched normal tissue sample.
SVanalyzer
Tools for the analysis of structural variation in genomes
nhansen's Repositories
nhansen/SVanalyzer
Tools for the analysis of structural variation in genomes
nhansen/Shimmer
Shimmer is a software package for the characterization of genetic differences between two very similar samples, e.g., a tumor sample and its matched normal tissue sample.
nhansen/bam2mpg
Software for calling variants from next-generation sequence data.
nhansen/MMBVariantCalling
Scripts and updates for running the variant pipeline described in "Variant Calling From Next Generation Sequence Data" by Nancy F. Hansen
nhansen/q100bench
Software for comparing genome assemblies and read datasets to a benchmark genome like the Q100 project's HG002v1.0.1
nhansen/NovoGraph
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
nhansen/BardCNV
BardCNV calls copy number variants from next generation sequencing data.
nhansen/mlgenofeatures
nhansen/mlgenotype
Python package for training and using machine learning models to recognize structural variants using features of aligned short read data
nhansen/AlphaThal
Pipeline for retrieving reads from the Alpha Thalassemia region
nhansen/bioconda-recipes
Conda recipes for the bioconda channel.
nhansen/issue-dump
Place to send issues created in error
nhansen/issue-playground
Testing repository for issue templates and trigger to google sheet
nhansen/LateStageEECs
Statistical analysis software used in Rudd et al., "KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid 2 endometrial carcinomas"
nhansen/github_issues
Python software to create and retrieve GitHub issues and write spreadsheets to Google Sheets with issue metadata
nhansen/nhansen
nhansen/nhansen.github.io
Documentation for Nancy Hansen's software tools
nhansen/NHGRI-BW2
Software to automate tasks for performing biowulf2 analyses remotely from a different server.
nhansen/RFGenotypeManuscript2023
Scripts and data files for "Random forest classifiers trained on simulated data enable accurate short read-based genotyping of structural variants in the alpha thalassemia genomic region"
nhansen/SleepInbredPanel
nhansen/T2Tvariants
Code used for Aganezov et al., A complete reference genome improves analysis of human genetic variation. bioRxiv, 2021.