tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.

Differential expression detection

G T A T C G C T A
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…

G T A T C G C T A
Seurat
Desktop

Seurat

An R package designed for the analysis and visualization of single cell RNA-seq…

An R package designed for the analysis and visualization of single cell RNA-seq data. Seurat contains easy-to-use implementations of commonly used analytical techniques, including the identification…

G T A T C G C T A
SCDE
Desktop

SCDE Single-Cell Differential Expression

Implements a set of statistical methods for analyzing single-cell RNA-seq data.

Implements a set of statistical methods for analyzing single-cell RNA-seq data.

G T A T C G C T A
powsimR
Desktop

powsimR

Simulates and evaluates differential expression from bulk and especially…

Simulates and evaluates differential expression from bulk and especially single-cell RNA-seq data. powsimR can not only estimate sample sizes necessary to achieve a certain power, but also informs…

G T A T C G C T A
MAST
Desktop

MAST Model-based Analysis of Single-cell Transcriptomics

A flexible statistical framework for the analysis of single-cell RNA sequencing…

A flexible statistical framework for the analysis of single-cell RNA sequencing data. MAST is suitable for supervised analyses about differential expression of genes and gene modules, as well as…

G T A T C G C T A
D3E
Desktop
Web

D3E Discrete Distributional Differential Expression

A tool for identifying differentially-expressed genes, based on single-cell…

A tool for identifying differentially-expressed genes, based on single-cell RNA-seq data. D3E consists of two modules: one for identifying differentially expressed (DE) genes, and one for fitting the…

G T A T C G C T A
scDD
Desktop

scDD single-cell Differential Distributions

A method to characterize differences in expression in the presence of distinct…

A method to characterize differences in expression in the presence of distinct expression states within and among biological conditions. Using simulated and case study data, we demonstrate that the…

G T A T C G C T A
DTWscore
Desktop

DTWscore Dynamic Time Warping score

Provides significant advantages for inferring the potential cell types.…

Provides significant advantages for inferring the potential cell types. DTWscore is capable of managing unevenly and sparsely sampled time-series gene expression data without need for prior…

G T A T C G C T A
DEsingle
Desktop

DEsingle

Allows differential expression (DE) analysis of scRNA-seq data. DEsingle is…

Allows differential expression (DE) analysis of scRNA-seq data. DEsingle is based on Zero-Inflated Negative Binomial (ZINB) model. It separates observed zero values as two parts to roughly reflect…

G T A T C G C T A
zingeR
Desktop

zingeR Zero Inflated Negative binomial Gene Expression in R

Permits to proceed scRNA-seq differentially expressed (DE) analysis. zingeR…

Permits to proceed scRNA-seq differentially expressed (DE) analysis. zingeR identifies excess zeros and provides observation weights to unlock bulk RNA-seq pipelines for zero-inflation. It is based…

G T A T C G C T A
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…

G T A T C G C T A
conquer
Desktop

conquer

Provides gene expression estimation in multiple units. conquer is a collection…

Provides gene expression estimation in multiple units. conquer is a collection of consistently processed, analysis-ready public scRNA-seq data sets collected using full-length transcript library…

G T A T C G C T A
SpatialDE
Desktop

SpatialDE

Identifies and characterizes spatially variable genes. SpatialDE is based on…

Identifies and characterizes spatially variable genes. SpatialDE is based on Gaussian Process Regression (GPR) that decomposes the expression variability into a spatial and non-spatial component. It…

G T A T C G C T A
TASC
Desktop

TASC Toolkit for Analysis of Single Cell RNA-seq

Incorporates the technical parameters, which reflect cell-to-cell batch…

Incorporates the technical parameters, which reflect cell-to-cell batch effects, into a hierarchical mixture model to estimate the biological variance of a gene and detect differentially expressed…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.