Services

🧬 Single-Cell RNA-seq (scRNA-seq)

$4,000 – $8,000

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)
• Pathway enrichment (KEGG, GO)

Deliverables: Publication-ready figures and DEG tables. CellChat, SCENIC, and Trajectory Analysis available as add-on services.

🗺️ Spatial Transcriptomics

$5,000 – $10,000

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: Publication-ready spatial figures and gene expression maps with written biological interpretation.

📊 Bulk RNA-seq Reanalysis

$1,500 – $3,500

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: Publication-ready figures, DEG tables, and written biological summary.

🔬 Advanced Cell Type Annotation

$1,000 – $2,500

Standard annotation is included in the base scRNA-seq package. This add-on is for complex datasets requiring publication-grade, reviewer-level annotation with full biological justification.

• Multi-reference integration (Azimuth + custom references)
• Fine-grained subtype annotation (rare and ambiguous populations)
• Literature-supported marker gene curation
• Cross-condition annotation consistency
• Ambiguous cluster resolution with biological rationale
• Optional integration with external reference datasets

Best for: Immune datasets, tumor microenvironment, complex tissues, or any project where reviewer-level rigor is required.

Deliverables: High-confidence annotation with detailed written justification for each cell type call.

🔗 CellChat — Ligand-Receptor Interaction Analysis

$1,000 – $2,500

• 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

$1,000 – $2,500

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

🧭 Trajectory & Pseudotime Analysis

$1,500 – $3,000

Advanced multi-method trajectory analysis for robust, publication-ready pseudotime and lineage inference. Using three complementary methods provides cross-validated results that single-method approaches cannot.

• Monocle3 — pseudotime and branching trajectory inference
• Slingshot — lineage inference and smooth pseudotime curves
• PHATE — high-dimensional trajectory visualization with complex branching
• Cross-method validation and interpretation
• DEG analysis along pseudotime
• Publication-ready trajectory figures

Deliverables: Publication-ready trajectory figures with written biological interpretation.

💬 Consulting

$200/hr

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