SC1 – a tool for interactive web-based single cell RNA-Seq data analysis

Single cell RNA-Seq (scRNA-Seq) is critical for studying cellular function and phenotypic heterogeneity as well as the development of tissues and tumors. Here, University of Connecticut researchers present SC1 a web-based highly interactive scRNA-Seq data analysis tool. The tool presents an integrated workflow for scRNA-Seq analysis, implements a novel method of selecting informative genes based on Term-Frequency Inverse-Document-Frequency (TF-IDF) scores, and provides a broad range of methods for clustering, differential expression analysis, gene enrichment, interactive visualization, and cell cycle analysis. The tool integrates other single cell omics data modalities like TCR-Seq and supports several single cell sequencing technologies. In just a few steps, researchers can generate a comprehensive analysis and gain powerful insights from their scRNA-Seq data.


Flow diagram describing the different integrated processes of the single cell analysis workflow implemented in SC1.

Availability – SC1 is publicly accessible at

Moussa M, Mandoiu I. (2021) SC1: A Tool for Interactive Web-Based Single Cell RNA-Seq Data Analysis. bioRXiv [online preprint]. [abstract]

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