Single-cell RNA-Seq Expression Analysis

Single-cell RNA-Seq (scRNA-Seq) enables in-depth exploration of individual cells within heterogeneous samples, offering high-resolution gene expression profiles. Its applications span from tissue cell type diversity to monitoring cellular responses, making it indispensable in developmental biology, immunology, neuroscience, and cancer research.

Single-cell RNA-Seq expression Pipeline

A workflow designed to perform read alignment, quality controls, data normalization, dimensionality reduction, clustering and differential expression of Single-cell transcriptomic data. This versatile workflow can be used for the analysis of any species with a published reference transcriptome (human, mouse, etc). All the steps in the pipeline are based on open source reference bioinformatics tools, considered as standards for scRNA-Seq expression analysis.

  • FastQC: Quality controls of reads

  • STARsolo: Read alignment

  • Seurat: Single-cell gene expression exploration


The pipeline provides multiple interactive plots and tables to explore the analyzed data.

Quality control metrics for sequence reads

Top variable features

Principal component heatmaps

Jackstraw scores

Non-linear dimensional reduction

Differentially expressed features

  • Price: $30

    Average per analysis

  • Runtime: 2 hrs

    Average per analysis

Why BatchX

BatchX offers a serverless infrastructure for running bioinformatics analyses as a fully managed service. With the click of a button, off-load all your complex processing requirements to the cloud in a cost-effective, secure, and scalable way.

Take full control of your analysis

Our RNA-Seq pipeline gives you the flexibility to customize it to suit your needs. It's super easy to change any parameter and re-run the analysis with the click of a button.

Bioinformatics analysis made easy

Our no code environment gives you the freedom you need to run the RNA-Seq pipeline with zero coding required. Share your results with collaborators in a secure and private manner.

Custom support

Get instant assistance for any issue from our extended and experienced bioinformatics team through dedicated slack channels, emails, or conference calls.

Our users love us

BatchX has provided me with the autonomy I needed. I can now easily and rapidly perform analysis and review results. I know I can rely on their bioinformatics expertise when I need to. I feel I’m now more in control of my research studies.

Alberto Gonzalez

Researcher, VHIO

We were yearning for independence and shorter turnaround times. With BatchX we can decide when and how we perform our bioinformatics analysis and have our results instantly. Thank you, guys, for the support and for the platform! I now feel I have bioinformatics super powers!

Montse Vega

Researcher, Pompeu Fabra University

BatchX User Insights: Montse Vega

Montse’s investigation revolves around a topic that is intriguing and exciting: Aging. She has dedicated her postdoctoral efforts to study the process of aging, the factors that promote premature senescence as well as the mechanisms that may increase...