Instruction file imported from rahulsarate/scRNA-seq-for-tissue-fluidity (.github/instructions/r-standards.instructions.md). Copyright stays with the author.

R Coding Standards — scRNA-seq Wound Healing

Style

• Use snake_case for variables and functions: filtered_counts, run_deseq2()
• Use PascalCase for Seurat objects: wound_sobj, Fibroblast_sobj
• Indent with 2 spaces (Tidyverse convention)
• Max line length: 100 characters

Reproducibility

• Always start with set.seed(42)
• End every script with sessionInfo()
• Save objects as .rds using saveRDS(), not save()
• Load configs from configs/analysis_config.yaml using yaml::read_yaml()

Bioconductor Patterns

# Standard library loading order
library(Seurat)        # scRNA-seq framework
library(DESeq2)        # Differential expression
library(clusterProfiler)  # Enrichment analysis
library(org.Mm.eg.db)  # Mouse gene annotations
library(ggplot2)       # Plotting
library(ComplexHeatmap) # Heatmaps
library(EnhancedVolcano) # Volcano plots
library(harmony)       # Integration

Mouse-Specific

• Mitochondrial genes: pattern = "^mt-" (lowercase for mouse)
• Use org.Mm.eg.db for mouse gene annotations
• Gene symbols: proper mouse case (Krt14, Col1a1, not KRT14, COL1A1)

Output Rules

• Figures: ggsave("analysis/figures/name.pdf", width=8, height=6, dpi=300)
• Tables: write.csv(res, "analysis/de/results.csv", row.names=TRUE)
• Objects: saveRDS(sobj, "analysis/clustering/wound_sobj.rds")