Bioinformatics & Computational Biology | Molecular Genetics
Senior Bioinformatician @ UMass Medical School | haibo.liu@umassmed.edu
Comprehensive guide to creating Docker images that work seamlessly with Singularity/Apptainer, covering compatibility considerations, Dockerfile best practices, common pitfalls, and testing strategies for HPC environments.
A comprehensive hands-on tutorial for using DRAGMAP for alignment and GATK for variant calling from WGS/WES data, covering both somatic and germline workflows with complete command examples, filtering, annotation with AI tools, and prioritization strategies.
A comprehensive Pandas guide designed for R users, with side-by-side comparisons of data structures and operations between R and Pandas to facilitate smooth transition from R to Python.
Comprehensive comparison of single-cell type annotation tools covering reference-based, marker-based, and machine learning approaches, with practical guidance on when and how to use each method.
Comprehensive step-by-step guidelines for sequencing-based somatic variant analysis using WGS/WES data, from raw FASTQ files to prioritized variants using consensus-based multi-tool pipelines.
Comprehensive guide to creating publication-ready scientific figures, covering tools, techniques, and best practices for data visualization, figure assembly, annotation, and meeting journal requirements.
A beginner's guide to bulk RNA-seq data analysis covering the complete pipeline from raw reads to gene set enrichment, including quality control, alignment, quantification, differential expression, and functional analysis.
Essential Groovy syntax and examples specifically tailored for building sophisticated Nextflow pipelines, covering the most commonly used Groovy features in workflow development.
Best practices for using conda/mamba environments and Docker/Singularity containers in Nextflow pipelines, including building cross-platform images, dependency management, and ensuring reproducibility.
Best practices for creating and managing Nextflow configuration files, including nextflow_schema.json, modules.json, nextflow.config, HPC cluster configurations, AWS Batch configurations, and testing strategies.
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