Tutorial: Genome assembly and scaffolding of small eukaryotic genomes
Published:
Learn genome assembly and scaffolding techniques for small eukaryotic genomes using NOVOloci and hifiasm.
Tutorials
Notes and walkthroughs I have written up, mostly on reproducible workflows, cloud and HPC setups, and genomics analysis.
Tutorial: Deploying JBrowse 2 on AWS EC2
Published:
Complete guide to deploying JBrowse 2, a next-generation genome browser, on AWS EC2 instances.
Tutorial: Docker and singularity image containing R and Renv for package version control
Published:
Learn how to create reproducible R environments using Renv with Docker and Singularity containers.
Tutorial: Running RStudio using Docker for smoother collaboration
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Guide to setting up RStudio in Docker containers for consistent development environments across teams.
Tutorial: Running R on machine without administrator rights using Singularity
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Learn how to use Singularity to run R on HPC systems without administrator privileges.
Tutorial: Visualizing genomic tracks with Gviz
Published:
Plotting bigWig ChIP-seq tracks alongside gene models and an ideogram in R using Gviz.
Tutorial: TPM calculation with library size normalization
Published:
Calculating transcripts per million (TPM) from raw RNA-seq counts in R, with library size normalization using edgeR.