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  • Single Cell Transcriptomics Pipeline

Discover how individual cells contribute to biology

Uncover cellular diversity and gain deeper biological insights with a streamlined single-cell transcriptomics workflow. Upload your raw FASTQ files and let the platform automatically handle quality control, alignment, clustering, and cell annotation. Move beyond bulk averages to understand the behavior of individual cell populations with publication-ready visualizations and detailed cell-type analysis. 

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Trusted by industry-leading institutes

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Workflow

How It Works

Raw reads in. Clean cell matrices out.

Drop your FASTQ files and walk away. QC trimming alignment and doublet removal run automatically. Your data is clean before analysis even begins.

  • Automatically filters, trims, and cleans raw FASTQ files.

  • Maps sequence reads against reference genomes.

  • Converts raw sequence data into clean gene expression matrices.

Your clusters. Auto-identified.

Count matrices normalize then flow into PCA and UMAP. Cells group by expression. Marker genes label each cluster automatically. No manual work needed.

  • Identifies statistically significant, differentially expressed genes.

  • Evaluates biological variance using PCA plots and heatmaps.

  • Maps genes to functional biological and KEGG pathways.

Built for modern research sharing

UMAP plots violin plots and annotation tables all in one interactive HTML report. Download it. Share it. Submit i

  • Delivers clear visual reports for primary and downstream analysis.

  • Generates high-resolution, interactive figures for quick reviews.

  • Streams results to your dashboard as soon as the run finishes.

Clustered. Annotated. Ready to publish results!

UMAP plots, cell annotations, differential expression results, and pathway reports appear in your dashboard automatically once the pipeline finishes.

  • Achieve unmatched accuracy by automating IC reconciliation.
  • Gain full transparency through real-time status monitoring.
  • Ensure seamless integration with secure, flexible solutions.
Our Pipeline Modules

Every layer of single-cell analysis covered.

Cell QC and filtering

FASTQ files go through FastQC trimming STARsolo alignment and doublet detection so only high quality cells move into analysis.

Clustering and annotation

UMAP and Leiden clustering group similar cells automatically while marker genes and reference databases identify cell populations instantly.

Variant annotation

Differential expression and pathway analysis reveal changing genes across cell groups while pseudo-time tracks cell state transitions.

10K+

Samples analyzed

99%

Pipeline accuracy

<24h

Turnaround time

200+

Research teams

Customer stories

Over 6,000 happy customers worldwide

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Got Questions?

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Get Started

Ready to turn your raw sequencing data
into publication-ready results?