Hyunmin Kim (Brandon)'s repositories
hmkim.github.io
Introduce bioinformatics software based on github
aws-healthimaging-samples
Sample projects on working with AWS HealthImaging, an AWS service that allows you to store, analyze, and share medical images in the cloud at petabyte scale.
aws-parallelcluster-user-guide
The open source version of the AWS ParallelCluster User Guide.
bioconda-recipes
Conda recipes for the bioconda channel.
cloud-automation
Automation for standing up Gen3 commons
demultiplex
Sequana demultiplexing pipeline
docker-oneshot
Rstudio + Rpy2 + Jupyter
eks-workshop-sample-api-service-go
Sample Kubernetes service used in the EKS Workshop CI/CD CodePipeline module
emr-serverless-hail
Run Hail using Amazon EMR Serverless
fq2vcf
Bash scripts for fastq to vcf pipeline, written for USyd Artemis HPC.
ga4gh-wes-on-aws-healthomics
GA4GH WES on AWS HealthOmics enables customers to use GA4GH WES with AWS HealthOmics Workflows. This allows easy migration for GA4GH WES applications to use the computing scale, predictable pricing, and built-in security and compliance provided by AWS HealthOmics Workflows.
guidance-for-multi-modal-data-analysis-with-aws-health-and-ml-services
An end-to-end framework for storing, integrating, and analyzing multimodal HCLS data on AWS, using AWS HealthOmics, AWS HealthLake, AWS HealthImaging, Amazon SageMaker, Amazon Athena, Amazon QuickSight, and Amazon S3.
guidance-for-multi-omics-and-multi-modal-data-integration-and-analysis-on-aws
This guidance creates a scalable environment in AWS to prepare genomic, clinical, mutation, expression and imaging data for large-scale analysis and perform interactive queries against a data lake. The solution also demonstrates the use of Amazon Omics for multi-modal analysis.
hail
Cloud-native genomic dataframes and batch computing
istio
Connect, secure, control, and observe services.
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
nf-core-koreaworkshop
AWS nextflow workshop for the 19th Korean Genome Organization (KOGO) Winter Symposium (Jan 31. - Feb 1.)
ngsperl
NGS perl modules
quickstart-hail
Hail on AWS EMR Sample
rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
sm-kornlp
A collection of Korean NLP hands-on labs on Amazon SageMaker
snakemake-aws-parallelcluster-slurm
Snakemake 8 profile for running on AWS ParallelCluster with the Slurm scheduler
training
Nextflow training material
vep-lambda
AWS lambda for Ensembl VEP
wgs_std_viper
Simple workflow to map WGS data to reference genome according to GATK best practices