Category: HPC
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No More Command-Line Only: Run Jupyter Lab, RStudio, and VS Code Interactively in Your Browser on Any HPC Cluster with Pixi
This tutorial is contributed by Giang Nguyen, founder of G Labs, providing consulting, software development, infrastructure engineering, and bioinformatics services to support scalable research and production workflows. He helps teams design, build, and optimize cloud/HPC platforms, develop custom tools and pipelines, and deliver reproducible, production-ready solutions for data-intensive science. You have your scRNA-seq environment set
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Setting Up Single-Cell RNA-seq Analysis Environment with Pixi: 10x Faster Setup, Zero Version Conflicts
This tutorial is contributed by Giang Nguyen, founder of G Labs, providing consulting, software development, infrastructure engineering, and bioinformatics services to support scalable research and production workflows. He helps teams design, build, and optimize cloud/HPC platforms, develop custom tools and pipelines, and deliver reproducible, production-ready solutions for data-intensive science. Introduction: Why Environment Management Is Critical
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Build Once, Run Anywhere: Creating Portable NGS Analysis Environments with Docker
Never worry about “it works on my machine” again – create portable, reproducible NGS analysis environments Introduction: The Reproducibility Challenge in NGS Analysis Picture this scenario: you’ve spent weeks perfecting your ChIP-seq analysis pipeline on your local workstation. The results are beautiful, the workflow is smooth, and everything runs flawlessly. Then comes the moment of
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HPC Data Management for NGS Analysis: Storage, Transfer, and Sharing Best Practices
Introduction to Data Management on High-Performance Computing Systems High-Performance Computing (HPC) systems have become essential tools for Next-Generation Sequencing (NGS) data analysis. These powerful computing environments allow researchers to process and analyze massive genomic datasets that would be impossible to handle on standard desktop computers. However, working effectively with HPC systems requires understanding how to
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High Performance Computing (HPC) Job Submission Systems: A Beginner’s Guide to Slurm
Introduction: Understanding High Performance Computing Have you ever tried to run a program on your computer, only to find that it takes hours or even days to complete? Or perhaps you needed to analyze a huge dataset that wouldn’t even fit in your computer’s memory? These are the kinds of problems that High Performance Computing
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Categories
- bulk RNA-seq (27)
- chromatin accessibility (14)
- Database (4)
- Epigenetics (14)
- Genomics (10)
- HPC (5)
- Metagenomics (1)
- Quick Tips (1)
- RNA-seq (14)
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- Single Cell Sequencing (14)
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Recent Posts
- How to Analyze Single-Cell RNA-seq Data – Complete Beginner’s Guide Part 12: Build Gene Co-expression Networks Using hdWGCNA
- How to Analyze Single-Cell RNA-seq Data — Complete Beginner’s Guide Part 11: Copy Number Variation Analysis Using CopyKAT
- No More Command-Line Only: Run Jupyter Lab, RStudio, and VS Code Interactively in Your Browser on Any HPC Cluster with Pixi
- How to Analyze Single-Cell RNA-seq Data – Complete Beginner’s Guide Part 10: Cell-Cell Communication Analysis Using NicheNet
Tags
Alternative Splicing Analysis ATAC-seq BAM ChIP-seq chromatin accessibility CNV DESeq2 Differential Expression edgeR FASTQ GATK Mutect2 gene expression heatmap HOMER HPC Isoform limma MACS2 MAF miRNA miRNA-seq MSigDB Normalization peak calling RNA-seq SLURM somatic mutations Transcript VCF whole genome sequencing