BioTender-max 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
- Quality control (FastQC, MultiQC)
- Alignment (STAR, HISAT2) or pseudo-alignment (Salmon, kallisto)
- Quantification (featureCounts, Salmon quant)
- Normalization (DESeq2 vst/rlog, edgeR TMM)
- Differential expression (DESeq2, edgeR, limma-voom)
- Visualization (volcano plot, MA plot, heatmap)
- Pathway analysis (clusterProfiler GO/KEGG, GSEA)
scRNA-seq Analysis (Scanpy / Seurat)
- Quality control (filter cells: mito%, gene count, UMI count)
- Normalization (library size, log1p)
- Feature selection (highly variable genes)
- Dimensionality reduction (PCA → UMAP/tSNE)
- Clustering (Leiden, Louvain)
- Marker identification (Wilcoxon, t-test)
- Cell type annotation (manual markers or automated)
- Trajectory analysis (PAGA, diffusion pseudotime)
GWAS / Genomics
- Quality control (MAF, HWE, call rate, relatedness)
- Association testing (PLINK, REGENIE)
- Multiple testing correction (Bonferroni, FDR)
- Manhattan plot, Q-Q plot
- 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
| Format | Content | Tools |
|---|---|---|
| FASTQ | Raw sequencing reads | FastQC, Trimmomatic |
| BAM/SAM | Aligned reads | samtools, IGV |
| VCF | Variant calls | bcftools, GATK |
| h5ad | AnnData (scRNA-seq) | Scanpy |
| RDS | R object | Seurat, DESeq2 |
| BED | Genomic regions | bedtools |