Single-cell RNA sequencing data analysis bioinformatics software tools

The development of high-throughput RNA sequencing (RNA-seq) at the single-cell level has already led to profound new discoveries in biology, ranging from the identification of novel cell types to the study of global patterns of stochastic gene expression. Alongside the…

scRNA-seq analysis steps

Single-cell RNA sequencing data analysis bioinformatics software tools

Most Recent Tools

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AUCell
Desktop

AUCell Area Under a Cell

Identifies cells with active gene regulatory networks (GRNs) in single cell…

Identifies cells with active gene regulatory networks (GRNs) in single cell RNA-seq data. AUCell calculates the enrichment of the regulon as an area under the recovery curve (AUC) across the ranking…

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SCENIC
Desktop

SCENIC Single Cell rEgulatory Network Inference and Clustering

Allows to reconstruct gene regulatory networks (GRNs). SCENIC uses single-cell…

Allows to reconstruct gene regulatory networks (GRNs). SCENIC uses single-cell RNA-seq data to identify stable cell states. It analyzes all the co-expression modules using cis-regulatory motif…

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UNCURL
Desktop
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scImpute
Desktop

scImpute

Address the dropout events prevalent in scRNAseq data. scImpute is an…

Address the dropout events prevalent in scRNAseq data. scImpute is an imputation method that determines which values are affected by dropout events in data and performs imputation only on dropout…

Most Popular Tools

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DESeq
Desktop

DESeq

A method for differential analysis of RNA-sequencing count data, using…

A method for differential analysis of RNA-sequencing count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a…

Curators for scRNA-seq analysis

  • Haodong Chen's avatar image
    Haodong Chen
    Stanford Cardiovascular Institute,…
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