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Differential expression detection

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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…

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Monocle
Desktop

Monocle

Allows to analyze single-cell gene expression experiments. Monocle can realize…

Allows to analyze single-cell gene expression experiments. Monocle can realize differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. The…

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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…

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AltAnalyze
Desktop

AltAnalyze

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis.…

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess…

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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.

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SAMstrt
Desktop

SAMstrt

Provides the significance analysis of sequencing data with spike-in…

Provides the significance analysis of sequencing data with spike-in normalization.

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Scanpy
Desktop

Scanpy

Allows analysis of single-cell gene expression data. Scanpy integrates…

Allows analysis of single-cell gene expression data. Scanpy integrates preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing and simulation of…

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Linnorm
Desktop

Linnorm

Provides a linear model and normality based transformation method. Linnorm is…

Provides a linear model and normality based transformation method. Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIPseq count data or any large-scale count data. It transforms such…

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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…

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CountClust
Desktop

CountClust

Allows users to fit Grade of membership models (GoM) for clustering of RNA-seq…

Allows users to fit Grade of membership models (GoM) for clustering of RNA-seq gene expression count data. CountClust also provides tools to identify which genes are most distinctively expressed in…

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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…

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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…

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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…

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SCell
Desktop

SCell

An integrated software tool for quality filtering, normalization, feature…

An integrated software tool for quality filtering, normalization, feature selection, iterative dimensionality reduction, clustering and the estimation of gene-expression gradients from large…

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BPSC
Desktop

BPSC Beta-Poisson model for Single-Cell RNA-seq data analyses

A model for gene expression of single-cell RNA-seq data based on the…

A model for gene expression of single-cell RNA-seq data based on the beta-Poisson mixture model. BPSC addresses practical and realistic issues such as non-integer expression values or low expression…

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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…

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DESCEND
Desktop

DESCEND DEconvolution of Single Cell ExpressioN Distribution

Deconvolves the true cross-cell gene expression distribution from observed…

Deconvolves the true cross-cell gene expression distribution from observed scRNA-seq counts. DESCEND is a statistical method that quantifies the dependence between features of distribution and cell…

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DECENT
Desktop

DECENT Differential Expression with Capture Efficiency AdjustmeNT

Performs differential expression (DE) analysis on scRNA-seq data. DECENT…

Performs differential expression (DE) analysis on scRNA-seq data. DECENT estimates the number of molecules pre-dropout and works even when spike-ins are not available. It can adjust for the imperfect…

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PIVOT
Desktop

PIVOT Platform for Interactive analysis and Visualization Of Transcriptomics data

Allows users to analyze and visualize RNA-Seq data. PIVOT furnishes four mains…

Allows users to analyze and visualize RNA-Seq data. PIVOT furnishes four mains functionalities (i) a graphical interface that is able to wrap existing open source packages in a single user-interface…

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bigSCale
Desktop

bigSCale

Provides an analytical framework for the sensitive detection of population…

Provides an analytical framework for the sensitive detection of population markers and differentially expressed genes. bigSCale aims to improve detection in large scRNAseq datasets. The software uses…

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dropClust
Desktop

dropClust

Preserves distinct structural properties of the data. dropClust uses Locality…

Preserves distinct structural properties of the data. dropClust uses Locality Sensitive Hashing (LSH), a logarithmic-time algorithm to determine approximate neighborhood for individual…

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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…

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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…

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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…

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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…

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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…

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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…

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Granatum
Desktop

Granatum

Makes analysis more broadly accessible to researchers. Granatum is a web…

Makes analysis more broadly accessible to researchers. Granatum is a web browser based scRNAseq analysis pipeline that conveniently walks the users through various steps of scRNA-seq analysis. It has…

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switchde
Desktop

switchde

Models differential expression over pseudotime. switchde is a statistical…

Models differential expression over pseudotime. switchde is a statistical framework that allows inference of switch-like differential expression along single-cell trajectories. The software…

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SINCERA
Desktop

SINCERA SINgle CEll RNA-seq profiling Analysis

A generally applicable analytic pipeline for processing single-cell RNA-seq…

A generally applicable analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. SINCERA provides a panel of analytic tools for users to conduct data filtering,…

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BASiCS
Desktop

BASiCS Bayesian Analysis of Single-Cell Sequencing data

An integrated Bayesian hierarchical model where: (i) cell-specific…

An integrated Bayesian hierarchical model where: (i) cell-specific normalisation constants are estimated as part of the model parameters, (ii) technical variability is quantified based on spike-in…

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M3Drop
Desktop

M3Drop

An R package providing functions for fitting a modified Michaelis-Menten (MM)…

An R package providing functions for fitting a modified Michaelis-Menten (MM) equation to the pattern of dropouts observed in a single-cell sequencing experiment. Analyses based on the MM equation,…

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SCPattern
Desktop

SCPattern

An empirical Bayes model to characterize genes with expression changes in…

An empirical Bayes model to characterize genes with expression changes in ordered single cell RNA-seq experiments. SCPattern utilizes the non-parametrical Kolmogorov-Smirnov statistic, thus it has…

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ISOP
Desktop

ISOP ISOform-Patterns

A method for analysis and characterization of single-cell isoform-level gene…

A method for analysis and characterization of single-cell isoform-level gene expression data. ISOP enables analysis of single-cell preference, commitment and heterogeneity of isoform level…

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Sake
Web
Desktop

Sake Single-cell RNA-Seq Analysis and Klustering Evaluation

Helps to quickly navigate through the expression profile, using non-negative…

Helps to quickly navigate through the expression profile, using non-negative matrix factorization (NMF) method for unsupervised clustering. Sake is an R package that provides analysis for analyzing…

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Cell Ranger
Desktop

Cell Ranger

Processes Chromium single cell 3’ RNA-seq output to align reads, generates…

Processes Chromium single cell 3’ RNA-seq output to align reads, generates gene-cell matrices and performs clustering and gene expression analysis. Cell Ranger combines Chromium-specific algorithms…

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