Single-Cell RNA-seq (scRNA-seq)
End-to-end processing of single-cell transcriptome matrix files. Our pipelines handle quality filtering, doublets, batch correction, spatial co-localization, pathway activities, and pseudotime cell ordering with rigorous precision.
- Doublet removal & mitochondrial filtering controls
- Batch correction & multi-sample integration (Harmony, Harmony-Seurat)
- Cell annotation, GSEA pathways, & RNA velocity analysis
Pipeline Specifications
FASTQ, 10x cellranger count matrices, Parse/BD count files
Annotated Seurat object (.rds) or scanpy AnnData (.h5ad), high-DPI vector figures, methods log, markdown notebooks
5 - 10 Business Days
Docking Specifications
Receptor PDB/PDBQT/SDF structures, compound SMILES libraries
Conformational complex PDB/SDF files, interaction matrices, 2D/3D pocket interaction maps, PyMOL layouts
7 - 12 Business Days
Molecular Docking & Screening
Structure-based computer-aided drug design. We predict protein-ligand binding modes, generate grid coordinates, execute high-throughput virtual screening of chemical libraries, and conduct binding affinity free energy assessments.
- Ligand / Receptor grid box design optimization
- AutoDock Vina conformational pose simulations
- Binding free energy calculations (MM-GBSA / MM-PBSA)
Transcriptomics Consulting
We provide full bulk differential analysis and spatial profiling services. Map tissue transcripts, correlate gene expression gradients with architectural tissue sections, and extract key molecular markers.
- Bulk differential genes expression profiles (DESeq2, edgeR)
- Spatial transcriptomics registration (10x Visium integration)
- Pathway and gene set enrichment analyses (GSEA, KEGG, GO)
Pipeline Specifications
FASTQ raw reads, raw aligned transcript counts, Visium space ranger outputs
Fully annotated expression profiles, pathway tables, high-DPI volcano/heatmap figures, reproducible notebooks
4 - 8 Business Days
Service Inquiries & Compliance
Common questions wet-lab principal investigators and coordinators ask prior to launching analysis pipelines.
We accept raw sequence FASTQ formats (which we align using CellRanger or Salmon-Alevin) as well as processed count matrices (such as 10x feature-barcode matrices, Parse Biosciences CSV/MTX bundles, or BD Rhapsody tables). If your data is already loaded in standard formats, we accept `.rds` (Seurat) and `.h5ad` (Scanpy) files directly.
Absolutely. We operate strictly on open-science principles. Along with your final figures and datasets, we deliver fully commented, executable Jupyter Notebooks (Python) or R Markdown scripts. These files document every step, parameter threshold, batch factor, and seed value so any reviewer can re-run and reproduce your exact outputs.
Data integrity and security are of paramount importance. We execute strict Mutual Non-Disclosure Agreements (NDAs) prior to data transfer. Your data is uploaded via encrypted SSH/HTTPS protocols and processed in isolated local servers with no public internet exposure. We do not share, sell, or utilize your datasets for any training purposes.
Yes. While human and mouse datasets constitute the majority of our workload, we regularly build custom pipeline alignments for non-standard model organisms (such as Danio rerio, Drosophila, Arabidopsis, or specific microbial profiles). We will build custom genome index references based on your designated Ensembl or NCBI FASTA/GTF files.