Services

🧬 Single-Cell RNA-seq (scRNA-seq)

$2,000 – $5,000

Full pipeline analysis from raw Seurat/AnnData object or FASTQ files to final publication-ready deliverables.

• Quality control and preprocessing
• Dimensionality reduction (PCA, UMAP)
• Cell clustering and cell type annotation (manual + SingleR/Azimuth)
• Subpopulation identification and abundance analysis
• Differential expression (DEG) analysis between conditions
• Module scoring (UCell — inflammatory, stress, functional signatures)
• Trajectory inference (Monocle3)
• Ligand-receptor interaction analysis (CellChat)
• Transcription factor regulon analysis (SCENIC)
• Pathway enrichment (KEGG, GO)

Deliverables: Figures, DEG tables (Excel), annotated Seurat/AnnData object, R/Python code, written biological summary.

🗺️ Spatial Transcriptomics

$3,500 – $8,000

Spatial gene expression analysis that maps cell types and gene activity directly onto tissue sections.

• 10x Visium and Stereo-seq analysis
• Spatial clustering and cell type deconvolution
• Spatially variable gene identification
• Integration with scRNA-seq reference data
• Tissue domain segmentation
• Publication-ready spatial maps

Deliverables: Spatial figures, gene expression maps, written summary, code.

📊 Bulk RNA-seq Reanalysis

$1,000 – $2,500

Rigorous reanalysis of existing bulk RNA-seq data with corrected statistical approaches and publication-ready figures.

• DEG analysis with DESeq2 or edgeR
• Pathway enrichment (KEGG, GO, GSEA)
• Contamination analysis (cell-type specific gene filtering)
• Heatmaps, volcano plots, PCA plots
• Written results summary

Deliverables: DEG tables, figures, written summary, code.

🔗 CellChat — Ligand-Receptor Interaction Analysis

$500 – $1,500

• Cell-cell communication network inference
• Signaling pathway activity across cell types
• Comparison between conditions (e.g. disease vs control)
• Bubble plots, chord diagrams, heatmaps

🧩 SCENIC — Transcription Factor Regulon Analysis

$500 – $1,500

• Gene regulatory network inference
• Transcription factor activity scoring per cell
• Regulon heatmaps and UMAP overlays
• Condition-specific TF activity comparison

💬 Consulting

$200/hr

• Analysis strategy and pipeline design
• Code review and troubleshooting
• Result interpretation and biological insight
• Manuscript figure review