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…
Desktop app
G T A T C G C T A Lag-based Expression… Lag-based Expression Association for…

LEAP Lag-based Expression Association for Pseudotime-series

Utilizes the estimated pseudotime of the cells to find gene co-expression that…

Utilizes the estimated pseudotime of the cells to find gene co-expression that involves time delay. LEAP sorts cells according to the estimated pseudotime and then computes the maximum correlation of…

Desktop app
G T A T C G C T A factorial single-cell… factorial single-cell Latent Variable Model

f-scLVM factorial single-cell Latent Variable Model

Uses gene set annotations to dissect single-cell transcriptome heterogeneity.…

Uses gene set annotations to dissect single-cell transcriptome heterogeneity. f-scLVM allows to identify biological drivers of cell-to-cell variability and model confounding factors. f-scLVM is…

Desktop app
G T A T C G C T A Je Je

Je

Offers tools to address most barcoding situations with and without unique…

Offers tools to address most barcoding situations with and without unique molecular identifier (UMI) and the identification of PCR duplicates based on extracted UMIs. In standard experimental set ups…

Desktop app
G T A T C G C T A nimfa nimfa

nimfa

A unified interface to matrix factorization algorithms and methods. Nimfa…

A unified interface to matrix factorization algorithms and methods. Nimfa includes published matrix factorization algorithms, initialization methods, quality and performance measures and facilitates…

Desktop app
G T A T C G C T A cellTree cellTree

cellTree

Produces tree structures outlining the hierarchical relationship between…

Produces tree structures outlining the hierarchical relationship between single-cell samples, while identifying latent groups of genes that can provide biological insights. CellTree can infer complex…

Desktop app
G T A T C G C T A Rare cell type… Rare cell type IDentification

RaceID Rare cell type IDentification

An algorithm for the identification of rare and abundant cell types from single…

An algorithm for the identification of rare and abundant cell types from single cell transcriptome data. RaceID is based on transcript counts obtained with unique molecular identifies. We demonstrate…

G T A T C G C T A Falco Falco

Falco

A cloud-based framework designed for multi-sample analysis of transcriptomic…

A cloud-based framework designed for multi-sample analysis of transcriptomic data in an efficient and scalable manner. Falco utilises state-of-the-art big data technology of Apache Hadoop and Apache…

Desktop app
G T A T C G C T A scater scater

scater

Contains useful tools for the analysis of single-cell gene expression data…

Contains useful tools for the analysis of single-cell gene expression data using the statistical software R. scater places an emphasis on tools for quality control, visualisation and pre-processing…

Desktop app
G T A T C G C T A scran scran

scran

Implements a variety of low-level analyses of single-cell RNA-seq data. Methods…

Implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly…

Desktop app
G T A T C G C T A CEL-Seq2 CEL-Seq2

CEL-Seq2

A modified version of our CEL-Seq method, with threefold higher sensitivity,…

A modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first…

Desktop app
G T A T C G C T A Single-cell RNA-seq… Single-cell RNA-seq Quality Control

SinQC Single-cell RNA-seq Quality Control

A method and software tool to detect technical artifacts in single-cell RNA-seq…

A method and software tool to detect technical artifacts in single-cell RNA-seq (scRNA-seq) samples by integrating both gene expression patterns and data quality information. SinQC assumes that if…

Desktop app
G T A T C G C T A FastProject FastProject

FastProject

A software package for two-dimensional visualization of single cell data, which…

A software package for two-dimensional visualization of single cell data, which utilizes a plethora of projection methods and provides a way to systematically investigate the biological relevance of…

Desktop app
G T A T C G C T A cellity cellity

cellity

A generic approach for processing scRNA-seq data and detecting low quality…

A generic approach for processing scRNA-seq data and detecting low quality cells, using a curated set of over 20 biological and technical features. cellity improves classification accuracy by over 30…

Desktop app
G T A T C G C T A Single-Cell Consensus… Single-Cell Consensus Clustering

SC3 Single-Cell Consensus Clustering

A tool for unsupervised clustering of single cell RNA-seq data. SC3 integrates…

A tool for unsupervised clustering of single cell RNA-seq data. SC3 integrates many different clustering solutions through a consensus approach, thereby increasing its accuracy and robustness against…

Desktop app
Web app
G T A T C G C T A Discrete… Discrete Distributional Differential Expression

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…

Web app
G T A T C G C T A Automated Single-cell… Automated Single-cell Analysis Pipeline

ASAP Automated Single-cell Analysis Pipeline

Aims at the complete analysis of scRNA-seq data post genome alignment: from the…

Aims at the complete analysis of scRNA-seq data post genome alignment: from the parsing, filtering, and normalization of the input count data files, to the visual representation of the data,…

Desktop app
G T A T C G C T A SSrGE SSrGE

SSrGE

A linear modeling framework that correlates genotype and phenotype information…

A linear modeling framework that correlates genotype and phenotype information in scRNA-seq data. SSrGE uses an accumulative ranking approach to select expressed nucleotide variations linked to the…

Desktop app
G T A T C G C T A schimera schimera

schimera

Tackles the polymerase chain reaction chimera problem in scRNA-seq by filtering…

Tackles the polymerase chain reaction chimera problem in scRNA-seq by filtering molecules that, for a given cell barcode and unique molecular identifier pair, have low read abundance.

Desktop app
G T A T C G C T A K-Branches K-Branches

K-Branches

Finds branching events and tips in single-cell data. K-Branches identifies the…

Finds branching events and tips in single-cell data. K-Branches identifies the exact number of branching regions, as well as the exact number of fully differentiated tip regions in the lineage tree.…

Desktop app
G T A T C G C T A Worm Single Cell Worm Single Cell

Worm Single Cell

Infers signalling networks at cellular level for cell fate specification based…

Infers signalling networks at cellular level for cell fate specification based on multiple data types, including single-cell gene expression data, PPI data, PDI data and Genetic Interaction (GI)…

G T A T C G C T A MicroArrayed… MicroArrayed Single-Cell sequencing

MASC-seq MicroArrayed Single-Cell sequencing

Enables massive microarray-based barcoding of expression patterns in single…

Enables massive microarray-based barcoding of expression patterns in single cells. MASC-seq allows both imaging and high-throughput single-cell analysis, characterizing thousands of single-cell…

Desktop app
G T A T C G C T A SCnorm SCnorm

SCnorm

A quantile regression method for accurate and efficient normalization of…

A quantile regression method for accurate and efficient normalization of scRNA-seq data. SCnorm uses quantile regression to estimate the dependence of read counts on sequencing depth for every gene.…

Desktop app
G T A T C G C T A BCR Assembly from… BCR Assembly from SIngle Cells

BASIC BCR Assembly from SIngle Cells

Allows investigators to use scRNA-seq for assembling BCR sequences at single…

Allows investigators to use scRNA-seq for assembling BCR sequences at single cell resolution. BASIC performs semi-de novo assembly in two stages: (i) uses known constant and variable regions to…

Web app
Desktop app
G T A T C G C T A SPRING SPRING

SPRING

A tool for uncovering high-dimensional structure in single-cell gene expression…

A tool for uncovering high-dimensional structure in single-cell gene expression data. From a table of gene expression measurement for single-cells, SPRING is able to build a k-nearest neighbor (knn)…

Desktop app
G T A T C G C T A SCODE SCODE

SCODE

An efficient regulatory network interference algorithm from single-cell RNA-Sep…

An efficient regulatory network interference algorithm from single-cell RNA-Sep during differentiation. SCODE is an algorithm interfering the regulatory networks, based on ordinary differential…

G T A T C G C T A Archetypal analysis… Archetypal analysis for cell type identificaTION

ACTION Archetypal analysis for cell type identificaTION

A method to project cells onto the state space of functional profiles,…

A method to project cells onto the state space of functional profiles, classifying them according to their principal functions, and reconstructing cell type-specific regulatory networks. ACTION…

Desktop app
G T A T C G C T A nbCopy Number Variants nbCopy Number Variants

nbCNV nbCopy Number Variants

A package to detect CNVs from over-dispersed sequencing data such as…

A package to detect CNVs from over-dispersed sequencing data such as single-cell sequencing (SCS) data. The nbCNV method uses two constraints-sparsity and smoothness to fit the CNV patterns under the…

Desktop app
G T A T C G C T A Unique Molecular… Unique Molecular IdentifierS

UMIS Unique Molecular IdentifierS

A uniform raw data processing pipeline to assessed the sensitivity and accuracy…

A uniform raw data processing pipeline to assessed the sensitivity and accuracy of many published scRNA­seq protocols based on standardized spike-¬ins. A flexible and fast unique molecular…

Desktop app
G T A T C G C T A PlateEffects2016 PlateEffects2016

PlateEffects2016

A package for the summation of counts across all cells on each plate for each…

A package for the summation of counts across all cells on each plate for each gene. The count sums can then be used in a differentially expressed (DE) analysis, effectively treating plates as…

Desktop app
G T A T C G C T A scVEGs scVEGs

scVEGs

An algorithm for single-cell RNA-seq data to determine significant variably…

An algorithm for single-cell RNA-seq data to determine significant variably expressed genes (VEGs) using a gene expression variation model (GEVM). scVEGs utilizes the relation between coefficient of…

Desktop app
G T A T C G C T A t-distributed… t-distributed Stochastic Neighbor Embedding

t-SNE t-distributed Stochastic Neighbor Embedding

A technique for dimensionality reduction that is particularly well suited for…

A technique for dimensionality reduction that is particularly well suited for the visualization of high-dimensional datasets. The technique can be implemented via Barnes-Hut approximations, allowing…

Desktop app
G T A T C G C T A Clustering through… Clustering through Imputation and Dimensionality…

CIDR Clustering through Imputation and Dimensionality Reduction

An ultrafast algorithm which uses a novel yet very simple "implicit…

An ultrafast algorithm which uses a novel yet very simple "implicit imputation" approach to alleviate the impact of dropouts in single cell RNA-seq (scRNA-seq) data in a principled manner.…

G T A T C G C T A switchde switchde

switchde

An R package for detecting switch-like differential expression along…

An R package for detecting switch-like differential expression along single-cell RNA-seq trajectories. Switchde assumes genes follow a sigmoidal pattern of gene expression and tests for differential…

Desktop app
G T A T C G C T A Scphaser Scphaser

Scphaser

An R package that phases alleles at heterozygous variants to reconstruct…

An R package that phases alleles at heterozygous variants to reconstruct haplotypes within transcribed regions of the genome using scRNA-seq data. Scphaser efficiently and accurately reconstructed…

Desktop app
G T A T C G C T A M3Drop M3Drop

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,…

Desktop app
G T A T C G C T A clusterExperiment clusterExperiment

clusterExperiment

Provides functions for running and comparing many different clusterings of…

Provides functions for running and comparing many different clusterings of single-cell sequencing data.

Desktop app
G T A T C G C T A hocuspocus hocuspocus

hocuspocus

Provides an easy-to-use and intuitive workflow for basic analysis of…

Provides an easy-to-use and intuitive workflow for basic analysis of single-cell RNA-Seq data. hocuspocus combines custom functions with functions from available packages. Particular emphasis is…

Desktop app
G T A T C G C T A Single-Cell Overview… Single-Cell Overview of Normalized Expression

SCONE Single-Cell Overview of Normalized Expression

An R package for single-cell RNA-seq data quality control and normalization.…

An R package for single-cell RNA-seq data quality control and normalization. This data-driven framework uses summaries of expression data to assess the efficacy of normalization workflows.

Desktop app
G T A T C G C T A scTCRseq scTCRseq

scTCRseq

A pipeline for single-cell RNA-seq package for recovering TCR data.

A pipeline for single-cell RNA-seq package for recovering TCR data.

Desktop app
G T A T C G C T A slingshot slingshot

slingshot

An R package for ordering single-cell sequencing. slingshot provides functions…

An R package for ordering single-cell sequencing. slingshot provides functions for determining lineage structure and ordering cellular progressions in single-cell sequencing data.

Desktop app
G T A T C G C T A GiniClust GiniClust

GiniClust

A tool for detecting rare cell types in normal tissues and disease samples and…

A tool for detecting rare cell types in normal tissues and disease samples and will facilitate the analysis of single-cell data. GiniClust outperforms RaceID for both simulated and biological…

G T A T C G C T A Cell-centric… Cell-centric statistics

Cell-centric statistics

An analytic framework that models transcriptome dynamics through the analysis…

An analytic framework that models transcriptome dynamics through the analysis of aggregated cell-cell statistical distances within biomolecular pathways. Within an elaborate case study of circulating…

Desktop app
G T A T C G C T A cgCorrect cgCorrect

cgCorrect

A method to correct for cell growth in single-cell transcriptomics data. We…

A method to correct for cell growth in single-cell transcriptomics data. We derive the probability for the cell growth corrected mRNA transcript number given the measured, cell size dependent mRNA…

Desktop app
G T A T C G C T A Single-Cell… Single-Cell expression data during…
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G T A T C G C T A Selective Locally… Selective Locally Linear Inference of Cellular…

SLICER Selective Locally Linear Inference of Cellular Expression Relationships

A method for inferring cellular trajectories from single cell RNA-seq data.…

A method for inferring cellular trajectories from single cell RNA-seq data. SLICER uses locally linear embedding to reconstruct cellular trajectories. SLICER provides four significant advantages over…

Desktop app
G T A T C G C T A densityCut densityCut

densityCut

A density-based clustering algorithm, which is both time- and space-efficient…

A density-based clustering algorithm, which is both time- and space-efficient and proceeds as follows: densityCut first roughly estimates the densities of data points from a K-nearest neighbour graph…

Desktop app
G T A T C G C T A Ensemble Cell Lineage… Ensemble Cell Lineage Analysis with Improved…

Eclair Ensemble Cell Lineage Analysis with Improved Robustness

A computational method for the statistical inference of cell lineage…

A computational method for the statistical inference of cell lineage relationships from single-cell gene expression data. ECLAIR uses an ensemble approach to improve the robustness of lineage…

Desktop app
G T A T C G C T A SCell SCell

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…

Desktop app
G T A T C G C T A Beta-Poisson model… Beta-Poisson model for Single-Cell RNA-seq data…

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…

Desktop app
G T A T C G C T A pQ (pseudocounted… pQ (pseudocounted Quantile)/NODES

pQ (pseudocounted Quantile)/NODES

A normalization technique that substantially reduces technical variability and…

A normalization technique that substantially reduces technical variability and improves the quality of downstream analyses. pQ homogenizes the expression of all genes below a fixed rank in each cell.…

Desktop app
G T A T C G C T A SCPattern SCPattern

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…

Desktop app
G T A T C G C T A scPLS scPLS

scPLS

A statistical method that solves a key challenge in data normalization for…

A statistical method that solves a key challenge in data normalization for single cell RNA sequencing: controlling for the hidden confounding factors (e.g. batch effects, cell cycle effects etc.) and…

Desktop app
G T A T C G C T A VDJPuzzle VDJPuzzle

VDJPuzzle

A method to reconstruct the native TCRαβ from single cell RNA-seq data of…

A method to reconstruct the native TCRαβ from single cell RNA-seq data of Ag-specific T cells and then to link these with the gene expression profile of individual cells. The workflow allows…

Desktop app
G T A T C G C T A pcaReduce pcaReduce

pcaReduce

An unsupervised hierarchical clustering approach for the identification of…

An unsupervised hierarchical clustering approach for the identification of putative cell sub-populations from single-cell transcriptomics profiles. Clustering occurs in a linearly transformed…

Desktop app
G T A T C G C T A TraCeR TraCeR

TraCeR

A computational method to reconstruct full-length, paired T cell receptor (TCR)…

A computational method to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. TraCeR links T cell specificity with functional response by…

Desktop app
G T A T C G C T A Clustering on… Clustering on Transcript Compatibility Counts

Clustering on Transcript Compatibility Counts

Offers a universal, efficient and accurate solution for extracting information…

Offers a universal, efficient and accurate solution for extracting information from single-cell RNA-seq experiments. In the same way that single-cell analysis can be viewed as the ultimate resolution…

Desktop app
G T A T C G C T A ISOform-Patterns ISOform-Patterns

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…

Desktop app
G T A T C G C T A SingleSplice SingleSplice

SingleSplice

A tool for studying alternative splicing using single cell RNA-seq data.…

A tool for studying alternative splicing using single cell RNA-seq data. SingleSplice uses a statistical model to detect genes whose isoform usage varies more than expected from the effects of…

Desktop app
G T A T C G C T A single-cell… single-cell Differential Distributions

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…

Desktop app
G T A T C G C T A Seurat Seurat

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…

Desktop app
G T A T C G C T A BackSPIN BackSPIN

BackSPIN

A divisive biclustering method based on sorting points into neighborhoods…

A divisive biclustering method based on sorting points into neighborhoods (SPIN). In contrast to the SPIN algorithm which does not identify clusters, here the aim was to identify groups of…

Desktop app
G T A T C G C T A SINgle CEll RNA-seq… SINgle CEll RNA-seq profiling Analysis

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,…

Desktop app
G T A T C G C T A Single-cell… Single-cell Clustering Using Bifurcation Analysis

SCUBA Single-cell Clustering Using Bifurcation Analysis

A computational method for extracting lineage relationships from single-cell…

A computational method for extracting lineage relationships from single-cell gene expression data, and modeling the dynamic changes associated with cell differentiation. SCUBA draws techniques from…

Desktop app
G T A T C G C T A Sphinx Sphinx

Sphinx

Improves the detection of changes in the transcriptional heterogeneity pattern…

Improves the detection of changes in the transcriptional heterogeneity pattern of in single-cell RNA-seq data using two heterogeneity parameters: "burst proportion" and "burst…

Desktop app
G T A T C G C T A Oscope Oscope

Oscope

A statistical pipeline for identifying oscillatory genes in unsynchronized…

A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq experiments. Oscope capitalizes on the fact that cells from an unsynchronized population represent…

Desktop app
G T A T C G C T A OEFinder OEFinder

OEFinder

A statistical method and software to identify a sorted list of ordering effect…

A statistical method and software to identify a sorted list of ordering effect (OE) genes. OEFinder is available as an R package along with user-friendly graphical interface implementations that…

Desktop app
G T A T C G C T A destiny destiny

destiny

An easy to use R package allowing for easy creation and plotting of diffusion…

An easy to use R package allowing for easy creation and plotting of diffusion maps. Diffusion maps are a spectral method for non-linear dimension reduction and have recently been adapted for the…

Desktop app
G T A T C G C T A Bayesian Analysis of… Bayesian Analysis of Single-Cell Sequencing data

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…

Desktop app
G T A T C G C T A Sincell Sincell

Sincell

Implements a methodological toolbox allowing flexible workflows under such a…

Implements a methodological toolbox allowing flexible workflows under such a framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support…

Desktop app
G T A T C G C T A single-cell diffusion… single-cell diffusion map

single-cell diffusion map

A tool for analysing single-cell differentiation data. Diffusion maps use a…

A tool for analysing single-cell differentiation data. Diffusion maps use a distance metric conceptually relevant to how differentiation data is generated biologically, as cells follow noisy…

Desktop app
G T A T C G C T A Model-based Analysis… Model-based Analysis of Single-cell…

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…

Desktop app
G T A T C G C T A Zero Inflated Factor… Zero Inflated Factor Analysis

ZIFA Zero Inflated Factor Analysis

Single cell RNA-seq data allows insight into normal cellular function and…

Single cell RNA-seq data allows insight into normal cellular function and diseases including cancer through the molecular characterisation of cellular state at the single-cell level. Dimensionality…

Desktop app
G T A T C G C T A GRM GRM

GRM

A major roadblock towards accurate interpretation of single cell RNA-seq data…

A major roadblock towards accurate interpretation of single cell RNA-seq data is large technical noise resulted from small amount of input materials. The existing methods mainly aim to find…

Desktop app
G T A T C G C T A Kinetics of… Kinetics of transcription

Kinetics of transcription

A statistical framework for studying the kinetics of stochastic gene expression…

A statistical framework for studying the kinetics of stochastic gene expression from single-cell RNA-seq data. The proposed statistical model provides a flexible and efficient way to investigate the…

Desktop app
G T A T C G C T A single-cell Latent… single-cell Latent Variable Model

scLVM single-cell Latent Variable Model

A modelling framework for single-cell RNA-seq data that can be used to dissect…

A modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of…

Desktop app
G T A T C G C T A Single-cell… Single-cell normalization

Single-cell normalization

A quantitative statistical method to distinguish true biological variability…

A quantitative statistical method to distinguish true biological variability from the high levels of technical noise in single-cell experiments. This approach quantifies the statistical significance…

Desktop app
G T A T C G C T A SNN-Cliq SNN-Cliq

SNN-Cliq

A clustering method designed for high dimensional gene expression data, e.g.…

A clustering method designed for high dimensional gene expression data, e.g. single-cell transcriptome data. This method can effectively cluster individual cells based on their transcriptomes,…

Desktop app
G T A T C G C T A Monocle Monocle

Monocle

A toolkit for analyzing single-cell gene expression experiments. It was…

A toolkit for analyzing single-cell gene expression experiments. It was designed for RNA-Seq, but can also work with single cell qPCR. It performs differential expression analysis, and can find genes…

Desktop app
G T A T C G C T A Single-Cell… Single-Cell Differential Expression

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.

Desktop app
G T A T C G C T A SAMstrt SAMstrt

SAMstrt

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

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

Web app
Desktop app
G T A T C G C T A Tools for Single Cell… Tools for Single Cell ANalysis

TSCAN Tools for Single Cell ANalysis

A software tool developed to better support in silico pseudo-time…

A software tool developed to better support in silico pseudo-time reconstruction in single-cell RNA-seq analysis. TSCAN uses a cluster-based minimum spanning tree (MST) approach to order cells. Cells…

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Desktop app
G T A T C G C T A Single-Cell Regulome… Single-Cell Regulome Analysis Tool

SCRAT Single-Cell Regulome Analysis Tool

Provides essential tools for users to read in single-cell regolome data…

Provides essential tools for users to read in single-cell regolome data (ChIP-seq, ATAC-seq, DNase-seq) and summarize into different types of features. SCRAT also allows users to visualize the…

Web app
Desktop app
G T A T C G C T A Single-Cell Gene… Single-Cell Gene Expression Pattern Analysis

SEPA Single-Cell Gene Expression Pattern Analysis

Provides convenient functions for users to assign genes into different gene…

Provides convenient functions for users to assign genes into different gene expression patterns such as constant, monotone increasing and increasing then decreasing. SEPA then performs GO enrichment…

G T A T C G C T A single-cell… single-cell interpretation via multi-kernel…

SIMLR single-cell interpretation via multi-kernel learning

A similarity-learning framework, which learns an appropriate distance metric…

A similarity-learning framework, which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization. SIMLR separates subpopulations more accurately in…

Desktop app
G T A T C G C T A Weighted-log-likelihood expectation maximization…

Curators for scRNA-seq analysis

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