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Mar 19, 2026

skills/bio/bioinformatics/SKILL.md

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Bioinformatics Analysis

Overview

Computational biology and genomics analysis pipelines. GENERAL: not locked to any specific tool — use Scanpy, Seurat, DESeq2, or any appropriate package.

Common Workflows

RNA-seq Analysis

  1. Quality control (FastQC, MultiQC)
  2. Alignment (STAR, HISAT2) or pseudo-alignment (Salmon, kallisto)
  3. Quantification (featureCounts, Salmon quant)
  4. Normalization (DESeq2 vst/rlog, edgeR TMM)
  5. Differential expression (DESeq2, edgeR, limma-voom)
  6. Visualization (volcano plot, MA plot, heatmap)
  7. Pathway analysis (clusterProfiler GO/KEGG, GSEA)

scRNA-seq Analysis (Scanpy / Seurat)

  1. Quality control (filter cells: mito%, gene count, UMI count)
  2. Normalization (library size, log1p)
  3. Feature selection (highly variable genes)
  4. Dimensionality reduction (PCA → UMAP/tSNE)
  5. Clustering (Leiden, Louvain)
  6. Marker identification (Wilcoxon, t-test)
  7. Cell type annotation (manual markers or automated)
  8. Trajectory analysis (PAGA, diffusion pseudotime)

GWAS / Genomics

  1. Quality control (MAF, HWE, call rate, relatedness)
  2. Association testing (PLINK, REGENIE)
  3. Multiple testing correction (Bonferroni, FDR)
  4. Manhattan plot, Q-Q plot
  5. Fine-mapping, colocalization

Key Databases

  • GEO (Gene Expression Omnibus): public expression datasets
  • TCGA (The Cancer Genome Atlas): cancer genomics
  • GTEx (Genotype-Tissue Expression): tissue-specific expression
  • ClinVar: clinical variant interpretations
  • UniProt: protein sequences and annotations
  • Ensembl: genome annotation

File Formats

FormatContentTools
FASTQRaw sequencing readsFastQC, Trimmomatic
BAM/SAMAligned readssamtools, IGV
VCFVariant callsbcftools, GATK
h5adAnnData (scRNA-seq)Scanpy
RDSR objectSeurat, DESeq2
BEDGenomic regionsbedtools

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