Useful R/RStudio Extensions

This guide covers essential R and RStudio extensions that will enhance your bioinformatics workflow and make working with the tucca-rna-seq results more efficient and enjoyable.

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Essential RStudio Extensions

1. Code Quality and Productivity

🔍 Code Diagnostics

Improve code quality and catch errors early.

• lintr: R code linting
• styler: Code formatting
• goodpractice: Best practices checker

⚡ Productivity Tools

Speed up your coding workflow.

• usethis: Package development tools
• devtools: Development utilities
• roxygen2: Documentation generation

2. Data Science and Visualization

📊 Data Manipulation

Essential packages for data analysis.

• tidyverse: Data science ecosystem
• data.table: Fast data operations
• dplyr: Data manipulation verbs

🎨 Visualization

Create publication-ready plots.

• ggplot2: Grammar of graphics
• plotly: Interactive plots
• patchwork: Plot composition

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Bioinformatics-Specific Extensions

1. Bioconductor Core

# Install Bioconductor
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

# Core packages
BiocManager::install(c(
    "Biobase",
    "BiocGenerics",
    "S4Vectors",
    "IRanges"
))

2. RNA-Seq Analysis

# Differential expression
BiocManager::install(c(
    "DESeq2",
    "edgeR",
    "limma"
))

# Quality control
BiocManager::install(c(
    "fastqcr",
    "ShortRead",
    "Biostrings"
))

3. Functional Enrichment

# Enrichment analysis
BiocManager::install(c(
    "clusterProfiler",
    "enrichplot",
    "DOSE"
))

# Pathway analysis
BiocManager::install(c(
    "pathview",
    "SPIA",
    "ReactomePA"
))

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RStudio IDE Extensions

1. Code Navigation

• Bookmarks: Mark important code sections
• Breadcrumbs: Navigate file structure
• Code Outline: View function structure
• Find in Files: Search across project

2. Version Control

• Git Integration: Built-in Git support
• Git History: View file changes
• Git Branches: Manage branches
• Pull Requests: GitHub integration

3. Project Management

• Project Templates: Standardize project structure
• R Markdown: Dynamic documents
• Shiny Apps: Interactive applications
• Package Development: Build R packages

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Installation and Setup

1. Install R and RStudio

# macOS (using Homebrew)
brew install --cask r
brew install --cask rstudio

# Ubuntu/Debian
sudo apt-get install r-base r-base-dev
# Download RStudio from https://posit.co/download/rstudio-desktop/

2. Install Essential Packages

# Core packages
install.packages(c(
    "tidyverse",
    "devtools",
    "usethis",
    "roxygen2"
))

# Bioconductor
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c(
    "DESeq2",
    "clusterProfiler",
    "pcaExplorer",
    "GeneTonic"
))

3. Configure RStudio

# Set working directory
setwd("~/path/to/your/project")

# Load common libraries
library(tidyverse)
library(DESeq2)
library(clusterProfiler)

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Best Practices

1. Project Organization

project/
├── data/
│   ├── raw/
│   └── processed/
├── scripts/
│   ├── analysis.R
│   └── functions.R
├── results/
│   ├── figures/
│   └── tables/
├── docs/
└── .Rproj

2. Code Style

# Use consistent naming
gene_counts <- read.csv("data/gene_counts.csv")
deseq_results <- run_deseq(gene_counts)

# Add comments
# Load differential expression results
deseq_results <- readRDS("results/deseq_results.RDS")

# Use pipe operator for readability
results_summary <- deseq_results %>%
    filter(padj < 0.05) %>%
    arrange(desc(log2FoldChange)) %>%
    head(100)

3. Reproducibility

# Set random seed
set.seed(42)

# Use renv for package management
renv::init()
renv::snapshot()

# Document session info
sessionInfo()

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Troubleshooting

Common Issues

Problem	Solution
Package conflicts	Use conflicts() to check
Memory issues	Increase memory limit in RStudio
Version conflicts	Use renv for isolation
Bioconductor errors	Update BiocManager

Getting Help

• R Help: ?function_name
• Package Vignettes: browseVignettes("package_name")
• Stack Overflow: [r] tag
• Bioconductor Support: support.bioconductor.org

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Next Steps

After setting up your R environment:

1. Explore the workflow results using the provided RMarkdown notebooks
2. Customize your analysis with additional R packages
3. Create publication-ready figures using ggplot2 and extensions
4. Share your code using version control and documentation

For workflow-specific analysis, see the Interactive Analysis guide.

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These extensions will significantly enhance your R/RStudio experience and make bioinformatics analysis more efficient and enjoyable.