Cheat Sheets

Quick, one- or two-page references that pair well with the workshop modules and the prerequisite appendices. Keep the relevant one open in a second tab while you work a tutorial — they’re for looking things up, not reading cover-to-cover.

The sheets follow the workshop’s toolchain: HPC & the cluster first, then the R language & command line, the plotting & rendering libraries, authoring & version control, the differential expression & enrichment tools, and finally the single-cell frameworks the modules are built on.

HPC, SLURM & the cluster (Talapas track)

• SLURM command & flag cheat sheet (official two-page summary) — sbatch/srun/squeue/sacct and the #SBATCH directives used in Modules 09–10.
• UO Talapas Quick Start Guide — the UO-specific account, partition, and module reference.
• Talapas Knowledge Base — how-to articles, FAQs, and partition details for UO’s cluster.
• module / Lmod quick reference — module avail / load / spider for the software-module system.
• See also Chapter 09 — VS Code & SLURM Basics on Talapas (connecting with VS Code Remote-SSH, interactive sessions, SLURM job submission).

R language & the command line

• Base R Cheat Sheet — the core language: vectors, indexing, control flow, apply.
• RStudio Collection of Cheat Sheets — the canonical index; the tidyverse family (dplyr, tidyr, purrr, stringr…) all live here.
• Advanced R reference (functions, environments) — scoping, the apply family, and S3/S4, which Seurat and Bioconductor objects use heavily.
• Common shell commands — Software Carpentry Unix reference — pwd/ls/cd, wildcards, pipes & redirection, grep/head/cut for inspecting data files.
• ss64 Bash command reference — a searchable A–Z of every shell command and its flags.
• See also the P2 — R & RStudio reading, Appendix H — Core R Commands, and Appendix C — grep/regex/shell.

Plotting & rendering

• ggplot2 Cheat Sheet — the grammar of graphics behind every figure in the tutorials.
• dplyr Data Transformation Cheat Sheet — filter/mutate/group_by/summarise, used throughout the marker and DE steps.
• tidyr Data Tidying Cheat Sheet — pivot_longer/pivot_wider for reshaping result tables.
• patchwork quick reference — composing multi-panel figures (p1 | p2, + plot_layout()).
• Color palettes — RColorBrewer & viridis — colorblind-safe palettes for cluster and expression plots.

Authoring, reproducibility & version control

• Quarto / Markdown Basics — the markup the tutorials and this site are written in.
• RStudio Quarto Cheat Sheet (PDF) — chunk options, YAML headers, output formats.
• Git Cheat Sheet — clone/commit/branch/push, the daily workflow.
• LaTeX Math Cheat Sheet — for equations in chapters and methods sections.
• See also Appendix I — Quarto & Markdown Syntax, Appendix D — Git & GitHub, and Appendix G — Methods-Section Template.

Differential expression & enrichment

• DESeq2 vignette — the design-formula, results(), shrinkage (lfcShrink/apeglm) and MA-plot workflow behind the pseudobulk DE in Module 06.
• edgeR quick start (User’s Guide) — the DGEList → glmQLFit alternative to DESeq2 for count-based DE.
• clusterProfiler book — ORA and GSEA with enrichGO/gseGO, dotplots, and enrichment maps used in Module 07.
• fgsea quick reference — fast pre-ranked GSEA and the enrichment-score plot.
• Harmony quick start — the integration method used in Module 05 (RunHarmony, theta, convergence).

Single-cell frameworks

• Seurat command list — function-by-function quick reference for the workshop’s primary framework (Modules 01–08).
• Seurat cheatsheet (object structure & accessors) — assays, layers, Idents(), FetchData(), metadata.
• Bioconductor SingleCellExperiment quick reference — the SCE container used by muscData, miloR, and the OSCA ecosystem.
• Signac cheat sheet (scATAC) — chromatin assays, fragments, and gene-activity objects (Modules 12 & 15).
• Scanpy / AnnData quick reference — the Python equivalent, useful when reading cross-language tutorials.