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

Most recent bioinformatics tools

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kBET
Desktop

kBET k-nearest neighbour Batch Effect Test

Quantifies batch effects in single-cell RNA-sequencing (scRNA-seq) data. kBET…

Quantifies batch effects in single-cell RNA-sequencing (scRNA-seq) data. kBET allows users to study high-dimensional data without prior assumptions regarding statistical properties. It can be applied…

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VASC
Desktop

VASC deep Variational Autoencoder for scRNA-seq data

Analyzes and visualizes single cell RNA sequencing (scRNA-seq data). VASC is a…

Analyzes and visualizes single cell RNA sequencing (scRNA-seq data). VASC is a deep variational autoencoder can capture non-linear variations and automatically learn a hierarchical representation of…

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Dhaka
Desktop

Dhaka

Allows learning of the underlying biology of the cancer samples. Dhaka is a…

Allows learning of the underlying biology of the cancer samples. Dhaka is a variational autoencoder based single cell analysis tool that combines Bayesian inference with such unsupervised deep…

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SAIC
Desktop

SAIC Single cell RNA-seq analysis with iterative clustering

Detects the optimal set of signature genes to separate single cells into…

Detects the optimal set of signature genes to separate single cells into distinct groups. SAIC uses an iterative k-means clustering approach to perform an exhaustive search for the best signature…

Most popular analytical software

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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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