Create minimal R single-cell template with Seurat, SpatialExperiment, and Bioconductor setup

[Copilot]

This PR implements a complete minimal R single-cell RNA sequencing analysis template as requested in the issue. The template provides a ready-to-use foundation for single-cell analysis with proper package management and comprehensive documentation.

Key Features Added

Project Structure

• Required folders: R/, data/, outputs/, vignettes/ for organized project layout
• Package management: renv.lock with pinned versions of essential packages
• Documentation: Comprehensive README and directory-specific guides

Core Dependencies

The renv.lock file includes all requested packages with specific versions:

• Seurat (v4.3.0) - Primary single-cell analysis framework
• SpatialExperiment (v1.10.0) - Bioconductor package for spatial transcriptomics
• ggplot2 (v3.4.2) - Data visualization
• Bioconductor ecosystem packages (BiocGenerics, S4Vectors, etc.)
• Supporting packages: dplyr, Matrix, cowplot, patchwork

Analysis Framework

• R/analysis_functions.R: Modular functions for data loading, preprocessing, normalization, and quality control
• R/example_analysis.R: Complete workflow demonstrating the analysis pipeline
• vignettes/getting_started.Rmd: Step-by-step tutorial with code examples

Quick Start Guide

The README includes detailed instructions for:

1. Environment setup: renv::restore() for reproducible package installation
2. Basic usage: Loading libraries and running analysis workflows
3. Project structure: Clear explanation of each directory's purpose
4. Citations: Proper attribution for Seurat, SpatialExperiment, and other packages

Development Setup

• .gitignore: Configured for R projects, excluding build artifacts and large data files
• .Rprofile: Automatic renv activation
• renv/settings.dcf: Package management configuration

Usage Example

# Install dependencies
renv::restore()

# Load libraries
library(Seurat)
library(SpatialExperiment)
library(ggplot2)

# Source analysis functions
source("R/analysis_functions.R")

# Run example analysis
source("R/example_analysis.R")

The template is immediately functional and provides a solid foundation for single-cell RNA-seq analysis projects with reproducible package management through renv.

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