Code Snippets

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Here are code snippets for when you need a one-liner, a speed run, or a guide for a specific small task. Some of these are topics discussed at MCGOmics Bashes, others are scripts provided to address analytical quandaries experienced by group members.

At the moment this is pretty disorganized–many are pages I wrote on the wiki, and some are barebones programming scripts in R or bash. I take all responsibility for disorganization.

• Bandaging a metagenome-assembled-genomic bin (bash)
• Slurm job management, Bash profiles
• Finding duplicate files
• Parsing taxonomy of OTUs/ASVs (R)
• Evaluating significant differential abundance of ASVs using Kruskal-Wallis testing (R)
• Plotting abundance data in R using pheatmap (R)

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reach out to Sharon if you have any questions. also feel free to open an issue