Single-cell sequencing

With the Single Cell Analysis Module, you can easily analyze and interpret your scRNA-seq data on your laptop.

Single-cell sequencing

With the Single Cell Analysis Module, you can easily analyze and interpret your scRNA-seq data on your laptop.

Uncover biological discoveries

We're here to help biologists and bioinformaticians like you reveal complex and rare cell populations, uncover relationships between genes and analyze gene expression differences.

See popular applications
Analyze

Annotate and identify cell types in your single-cell NGS data with easy-to-use, robust tools and algorithms

Discover

Identify key biomarkers for cell types, tissues and diseases without the tedious work of curating and analyzing each dataset

Investigate

Explore the biological context of specific pathways, transcriptional drivers and disease states underlying your single-cell data

Everything you need for single-cell data processing

Gene expression
For scRNA-seq data from droplet-seq and combinatorial barcoding protocols
Immune repertoire
T or B cell receptors, clonotype prediction from scVDJ-seq (scTCR-seq, scBRC-seq) data
Cell type prediction
The module includes a pre-trained classifier that annotates individual cells. It has been trained on large human and mouse single-cell projects
Hashtag analysis
For CITE-seq, TotalSeq, BEAM and other types of data
UMAP and tSNE
Overlay our interactive 2D and 3D plots with cell, gene expression, velocity and peak matrix data
RNA velocity
For scoring velocity genes and creating phase portraits, which predicts the future state of individual cells in processes like embryogenesis and tissue regeneration
Spatial transcriptomics

For 10X Genomics® Visium Spatial Gene Expression data

Chromatin accessibility
For scATAC-seq data, including peak calling, nearby gene and transcription factor motif scans and QC reports
Droplet-seq

For 10X Genomics® Chromium data and more

Combinatorial barcoding

For protocols like Evercode™ from Parse Biosciences

Interested in our single-cell solutions?

Our suite of CLC modules and plugins has you covered, from analysis to investigation. 
What are other scientists doing?
See how CLC is accelerating single-cell discoveries around the world with our case studies, blogs, articles and more.
Browse the latest resources
Not sure where to start?
Our Services team is happy to help you with anything from individual single-cell projects to institution-wide research initiatives.
Processing and curation
Start your single-cell journey
We offer webinars on everything single-cell! Well, almost. Get started with one of our favorites.
Single-cell ATAC sequence workflows
Sample to Insight
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