Pinned Repositories
bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
toil-rnaseq
UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
toil
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
crawler
for web crawler
hmkim.github.io
Introduce bioinformatics software based on github
workflow
Workflow in bioinformatics
hmkim's Repositories
hmkim/hmkim.github.io
Introduce bioinformatics software based on github
hmkim/amazon-ecr-helper-for-aws-healthomics
hmkim/amazon-omics-tools
hmkim/amplify-vite-react-template
My Amplify Gen 2 starter application
hmkim/argo-data-submission
Workflow to submit genomic data to ARGO RDPC for processing
hmkim/aws-genomics-workflows
Genomics Workflows on AWS
hmkim/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.
hmkim/aws-healthomics-eventbridge-integration
hmkim/cloud-automation
Automation for standing up Gen3 commons
hmkim/ega-fuse-client
A Java/JNR based FUSE virtual file system client to provide access to authorized EGA files via the EGA Data REST API (v3)
hmkim/emr-serverless-hail
Run Hail using Amazon EMR Serverless
hmkim/emr-serverless-samples
Example code for running Spark and Hive jobs on EMR Serverless.
hmkim/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.
hmkim/gd-2023-may
hmkim/glow
An open-source toolkit for large-scale genomic analysis
hmkim/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.
hmkim/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.
hmkim/hail
Cloud-native genomic dataframes and batch computing
hmkim/healthomics-workflows
UltimaGenomics repository for workflows compatible with AWS HealthOmics
hmkim/nf-core-koreaworkshop
AWS nextflow workshop for the 19th Korean Genome Organization (KOGO) Winter Symposium (Jan 31. - Feb 1.)
hmkim/notion2bookstack
Publish document exported from Notion in markdown format to Bookstack. Images are also processed.
hmkim/quickstart-hail
Hail on AWS EMR Sample
hmkim/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
hmkim/scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
hmkim/sm-kornlp
A collection of Korean NLP hands-on labs on Amazon SageMaker
hmkim/snakemake-aws-parallelcluster-slurm
Snakemake 8 profile for running on AWS ParallelCluster with the Slurm scheduler
hmkim/stride-gpt
An AI-powered threat modeling tool that leverages OpenAI's GPT models to generate threat models for a given application based on the STRIDE methodology.
hmkim/training
Nextflow training material
hmkim/ultimate-rag
A modular and comprehensive solution to deploy a Multi-LLM and Multi-RAG powered chatbot (Amazon Bedrock, Anthropic, HuggingFace, OpenAI, Meta, AI21, Cohere) using AWS CDK on AWS
hmkim/vep-lambda
AWS lambda for Ensembl VEP