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…
G T A T C G C T A
scLVM
Desktop

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…

G T A T C G C T A
RaceID
Desktop

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
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
Monocle
Desktop

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…

G T A T C G C T A
BackSPIN
Desktop

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…

G T A T C G C T A
MIMOSCA
Desktop

MIMOSCA Multiple Input Multiple Output Single Cell Analysis

Allows to decipher the effect of individual perturbations and the marginal…

Allows to decipher the effect of individual perturbations and the marginal contributions of genetic interactions on the level of each transcript, program, and cell state. MIMOSCA was designed to…

G T A T C G C T A
TraCeR
Desktop

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…

G T A T C G C T A
Oscope
Desktop

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…

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
CEL-Seq
Desktop

CEL-Seq

CEL-Seq provides its first single-cell, on-chip barcoding method, and we…

CEL-Seq provides its first single-cell, on-chip barcoding method, and we detected gene expression changes accompanying the progression through the cell cycle in mouse fibroblast cells. The pipeline…

G T A T C G C T A
cellity
Desktop

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…

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

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…

G T A T C G C T A
TSCAN
Web
Desktop

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…

G T A T C G C T A
nimfa
Desktop

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…

G T A T C G C T A
SAMstrt
Desktop

SAMstrt

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

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

G T A T C G C T A
LEAP
Desktop

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…

G T A T C G C T A
Falco
Cloud

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…

G T A T C G C T A
SinQC
Desktop

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…

G T A T C G C T A
MASC-seq
Algorithm

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…

G T A T C G C T A
GiniClust
Desktop

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
SLICER
Desktop

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…

G T A T C G C T A
Clustering on…
Desktop

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…

G T A T C G C T A
NMFEM
Desktop

NMFEM

Analyzes a wide variety of scRNA-Seq datasets, ranging from mouse hematopoietic…

Analyzes a wide variety of scRNA-Seq datasets, ranging from mouse hematopoietic stem cells to human glioblastoma data. NMFEM generates protein-protein interaction (PPI) network modules from selected…

G T A T C G C T A
Eclair
Desktop

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…

G T A T C G C T A
SingleSplice
Desktop

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…

G T A T C G C T A
Batch Effect…
Desktop

Batch Effect Removal

Removes systematic batch effects. Batch Effect Removal is a method based on a…

Removes systematic batch effects. Batch Effect Removal is a method based on a residual neural network, trained to minimize the Maximum Mean Discrepancy (MMD) between the multivariate distributions of…

G T A T C G C T A
powsim
Desktop

powsim

Simulates and evaluates differential expression from bulk and especially…

Simulates and evaluates differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses. Powsim is a flexible tool that can not…

G T A T C G C T A
scRNASeqDB
Dataset

scRNASeqDB

Collects and curates gene expression profiles of the transcriptome of human…

Collects and curates gene expression profiles of the transcriptome of human single cells. scRNASeqDB provides various features such as gene expression in different cell types, expression patterns at…

G T A T C G C T A
Sincell
Desktop

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…

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
cellTree
Desktop

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…

G T A T C G C T A
FastProject
Desktop

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…

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
ZIFA
Desktop

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…

G T A T C G C T A
StemID
Desktop

StemID

Identifies stem cells among all detectable cell types within a population.…

Identifies stem cells among all detectable cell types within a population. StemID is an algorithm based on RaceID2 (Rare Cell Type Identification) an algorithm for the identification of rare and…

G T A T C G C T A
f-scLVM
Desktop

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…

G T A T C G C T A
SC3
Desktop

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…

G T A T C G C T A
Worm Single…
Desktop

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
BASIC
Desktop

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…

G T A T C G C T A
Scphaser
Desktop

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…

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

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…

G T A T C G C T A
densityCut
Desktop

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…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
OEFinder
Desktop

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…

G T A T C G C T A
destiny
Desktop

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…

G T A T C G C T A
LungGENS
Web

LungGENS Lung Gene Expression iN Single-cell

Facilitates the retrieval of lung cell-specific gene expression information…

Facilitates the retrieval of lung cell-specific gene expression information from extensive data sets derived from RNA sequencing of single cells. LungGENS is a web-based bioinformatics resource for…

G T A T C G C T A
VDJPuzzle
Desktop

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…

G T A T C G C T A
scVEGs
Desktop

scVEGs

Determines significant variably expressed genes (VEGs) using a gene expression…

Determines significant variably expressed genes (VEGs) using a gene expression variation model (GEVM). scVEGs utilizes the relation between coefficient of variation (CV) and average expression level…

G T A T C G C T A
ZINB-WaVE
Desktop

ZINB-WaVE

Leads to low-dimensional representations of the data that account for zero…

Leads to low-dimensional representations of the data that account for zero inflation (dropouts), over-dispersion, and the count nature of the data. ZINB-WaVE is a general and flexible zero-inflated…

G T A T C G C T A
BEARscc
Desktop

BEARscc Bayesian ERCC Assessment of Robustness

Simulates experiment-specific technical replicates. BEARscc improves the…

Simulates experiment-specific technical replicates. BEARscc improves the unsupervised classification of cells and facilitates the biological interpretation of single-cell RNA-seq experiments. It…

G T A T C G C T A
umis
Desktop

umis

Provides a way of removing amplification biases, the assumed absolute…

Provides a way of removing amplification biases, the assumed absolute quantification does not appear to hold true perfectly. Umis is a flexible tool for counting the number of unique molecular…

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…

G T A T C G C T A
GPfates
Desktop

GPfates

Models transcriptional cell fates as mixtures of the Gaussian Process Latent…

Models transcriptional cell fates as mixtures of the Gaussian Process Latent Variable Model and Overlapping Mixtures of Gaussian Processes (OMGP). GPfates is based on first reconstructing the…

G T A T C G C T A
MAGIC
Desktop

MAGIC Markov Affinity-based Graph Imputation of Cells

Provides a method for imputing missing values, and restoring the structure of…

Provides a method for imputing missing values, and restoring the structure of the data. After the use of MAGIC, two- and three-dimensional gene interactions are restored. MAGIC is able to impute…

G T A T C G C T A
SCALE
Desktop

SCALE Single Cell ALlelic Expression

Analyzes genome-wide allele-specific bursting. SCALE permits adjustment of…

Analyzes genome-wide allele-specific bursting. SCALE permits adjustment of technical variability. It detects genes exhibiting allelic differences in bursting parameters, and genes whose alleles burst…

G T A T C G C T A
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…

G T A T C G C T A
single-cell…
Desktop

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…

G T A T C G C T A
GRM
Desktop

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…

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

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,…

G T A T C G C T A
WemIQ
Desktop
G T A T C G C T A
Je
Desktop

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 polymerase chain reaction (PCR) duplicates based on extracted UMIs. In…

G T A T C G C T A
nbCNV
Desktop

nbCNV nbCopy Number Variants

Detect copy number variations (CNVs) from over-dispersed sequencing data such…

Detect copy number variations (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…

G T A T C G C T A
SCOUP
Desktop
G T A T C G C T A
pcaReduce
Desktop

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…

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

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…

G T A T C G C T A
t-SNE
Desktop

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…

G T A T C G C T A
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,…

G T A T C G C T A
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…

G T A T C G C T A
ASAP
Web

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,…

G T A T C G C T A
SSrGE
Desktop

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…

G T A T C G C T A
schimera
Desktop

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.

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

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.…

G T A T C G C T A
SCnorm
Desktop

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.…

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

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)…

G T A T C G C T A
SCODE
Desktop

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
ACTION
Algorithm

ACTION Archetypal analysis for cell type identificaTION

Projects cells onto the state space of functional profiles, classifying them…

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

G T A T C G C T A
UMIS
Desktop

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…

G T A T C G C T A
PlateEffects201…
Desktop

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…

G T A T C G C T A
CIDR
Desktop

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
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,…

G T A T C G C T A
cgCorrect
Desktop

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…

G T A T C G C T A
SIMLR
Algorithm

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…

G T A T C G C T A
Pseudocounted…
Desktop

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.…

G T A T C G C T A
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…

G T A T C G C T A
scPLS
Desktop

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…

G T A T C G C T A
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…

G T A T C G C T A
clusterExperime…
Desktop

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.

G T A T C G C T A
scater
Desktop

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…

G T A T C G C T A
SCONE
Desktop

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.

G T A T C G C T A
scran
Desktop

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…

G T A T C G C T A
Sphinx
Desktop

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…

G T A T C G C T A
SCUBA
Desktop

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…

G T A T C G C T A
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…

G T A T C G C T A
switchde
Library

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…

G T A T C G C T A
hocuspocus
Desktop

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…

G T A T C G C T A
scTCRseq
Desktop

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.

G T A T C G C T A
slingshot
Desktop

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.

G T A T C G C T A
SCRAT
Web
Desktop

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…

G T A T C G C T A
SEPA
Web
Desktop

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…

Curators for scRNA-seq analysis

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

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