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Other scRNA-seq data analysis tools

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RCA
Desktop

RCA Reference Component Analysis

Projects single-cell transcriptomes into a space defined by variability in a…

Projects single-cell transcriptomes into a space defined by variability in a reference data set. RCA is an R package for robust clustering analysis of single cell RNA sequencing data (scRNAseq). This…

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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…

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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…

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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…

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SLICE
Desktop

SLICE Single Cell Lineage Inference Using Cell Expression Similarity and Entropy

Allows to quantitatively measure differentiation states of individual cells and…

Allows to quantitatively measure differentiation states of individual cells and reconstruct their lineages from scRNA-seq data. SLICE consists of two major utilizations: measuring cell…

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WaveCrest
Desktop

WaveCrest

Allows to reconstruct the differentiation trajectory from the pluripotent state…

Allows to reconstruct the differentiation trajectory from the pluripotent state through mesendoderm to definitive endoderm (DE). WaveCrest permits to reorder single cells according to the expression…

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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…

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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…

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MATCHER
Desktop

MATCHER Manifold Alignment To CHaracterize Experimental Relationships

Characterizes corresponding transcriptomic and epigenetic changes in embryonic…

Characterizes corresponding transcriptomic and epigenetic changes in embryonic stem cells (ESCs). MATCHER gives insight into the sequential changes of genomic information. It allows the use of both…

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scran
Desktop

scran

Allows to perform several low-level analyses on of single-cell RNA-seq data.…

Allows to perform several low-level analyses on of single-cell RNA-seq data. Scran is a package that provides functions to normalize cell-specific biases, assign cell cycle phase, and detect highly…

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Falco
Desktop

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…

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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…

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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…

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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…

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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…

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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…

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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…

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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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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…

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SC3
Desktop

SC3 Single-Cell Consensus Clustering

Allows to cluster single cell RNA-seq data. SC3 integrates many different…

Allows to cluster single cell RNA-seq data. SC3 integrates many different clustering solutions through a consensus approach, thereby increasing its accuracy and robustness against noise. To enhance…

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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…

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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…

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JingleBells
Dataset

JingleBells

Facilitates the reutilization of immune-related scRNA-seq datasets ready for…

Facilitates the reutilization of immune-related scRNA-seq datasets ready for analysis and visualization of reads at the single-cell level. JingleBells provides data of publicly available…

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VDJPuzzle
Desktop

VDJPuzzle

Allows users to reconstruct the native T-cell receptors (TCR)αβ from single…

Allows users to reconstruct the native T-cell receptors (TCR)αβ from single cell RNA-seq data of Ag-specific T cells and to link these with the gene expression profile of individual cells.…

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MetaNeighbor
Desktop

MetaNeighbor Meta-analysis via Neighbor voting

Permits to compare, validate and substantiate cell type transcriptional…

Permits to compare, validate and substantiate cell type transcriptional profiles across scRNA-seq datasets. MetaNeighbor can readily identify cells of the same type across datasets, without relying…

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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…

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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)…

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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…

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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…

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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…

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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…

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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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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…

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FateID
Desktop

FateID

Quantifies fate bias, manifested by subtle lineage specific transcriptome…

Quantifies fate bias, manifested by subtle lineage specific transcriptome modulations within a multipotent progenitor population. FateID is based on prior knowledge and a random forests-based…

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CyteGuide
Web

CyteGuide

Guides and summarizes the hierarchical exploration of large single-cell data.…

Guides and summarizes the hierarchical exploration of large single-cell data. CyteGuide is an integrated visualization for that extends Hierarchical Stochastic Neighborhood Embedding (HSNE) by…

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velocyto
Desktop

velocyto

Assists users in the estimation of velocity and the related data analysis.…

Assists users in the estimation of velocity and the related data analysis. Velocyto is an analysis framework developed for the analysis of expression dynamics single cell RNA seq data. This analysis…

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TRAPeS
Desktop

TRAPeS TCR Reconstruction Algorithm for Paired-End Single-cell

Reconstructs T cell receptors (TCRs) from paired-end sequencing libraries of…

Reconstructs T cell receptors (TCRs) from paired-end sequencing libraries of single cells, even at short (25 bp) read length. TRAPeS is a software that works on the original reads - leading to…

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reCAT
Desktop

reCAT recover Cycle Along Time

Reconstructs cell cycle time-series using single-cell transcriptome data. reCAT…

Reconstructs cell cycle time-series using single-cell transcriptome data. reCAT is a computational method consists of four steps: (i) the data processing, including quality control, normalization,…

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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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HopLand
Desktop

HopLand

Provides a method based on a modeling of Waddington’s epigenetic landscape…

Provides a method based on a modeling of Waddington’s epigenetic landscape for retrieving pseudotimes from single-cell data. HopLand is a standalone software that does not depend on prior knowledge…

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DistMap
Desktop

DistMap

Offers a mapping strategy based on spatially distributed scores. DistMap is an…

Offers a mapping strategy based on spatially distributed scores. DistMap is an algorithm which uses measured gene expression and allows researchers to map single cell RNA sequencing data without…

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Citrus
Desktop

Citrus

Allows users to analyze single cell sequencing. Citrus is a toolkit that…

Allows users to analyze single cell sequencing. Citrus is a toolkit that provides two different methods. First scPLS, a statistical method considering both control and target genes, which permits…

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BGP
Desktop

BGP branching Gaussian process

Provides a method for identifying the branching times of individual genes. BGP…

Provides a method for identifying the branching times of individual genes. BGP is an open source software using a sparse variational inference and permits a defined parameter estimation via the…

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pCMF
Desktop

pCMF probabilistic Count Matrix Factorization

Provides factor model, takes advantage of the Poisson Gamma representation,…

Provides factor model, takes advantage of the Poisson Gamma representation, with the use of Gamma priors on the distribution of principal components. pCMF is a dimension reduction method that is…

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ascend
Desktop

ascend Analysis of Single Cell Expression, Normalisation and Differential expression

Allows creation of workflow for the analysis of Single cell RNA sequencing…

Allows creation of workflow for the analysis of Single cell RNA sequencing (scRNA-seq) experiments. ascend can handle data generated from any single cell library preparation platform. It includes…

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AGA
Desktop

AGA Approximate Graph Abstraction

Allows to reproduce analyses and figures of the publication. AGA offers an…

Allows to reproduce analyses and figures of the publication. AGA offers an algorithm that combines computational clustering and trajectory inference analysis strategies by explaining cell to cell…

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mcSCRB-seq
Desktop

mcSCRB-seq molecular crowding Single-Cell RNA-Barcoding and Sequencing

Improves the sensitivity and efficiency of Single-Cell RNA-Barconding and…

Improves the sensitivity and efficiency of Single-Cell RNA-Barconding and Sequencing (SCRB-seq). mcSCRB-seq is a highly flexible, fast and efficient library protocol with low set-up costs and hence…

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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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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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PerraudeauEtAl2…
Desktop

PerraudeauEtAl2017

Permits downstream analysis. This tool contains four steps: (1) dimensionality…

Permits downstream analysis. This tool contains four steps: (1) dimensionality reduction accounting for zero inflation and over-dispersion, and adjusting for gene and cell-level covariates; (2)…

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BraCeR
Desktop

BraCeR

Permits reconstruction of paired full-length B-cell receptor sequences and…

Permits reconstruction of paired full-length B-cell receptor sequences and inference of clonality from scRNA-seq data. BraCeR is an application that allows reconstruction of additional heavy and…

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SCRL
Desktop

SCRL Single Cell Representation Learning

Learns representations for scRNA-seq data by considering the prior gene–gene…

Learns representations for scRNA-seq data by considering the prior gene–gene association. SCRL is a data-driven and nonlinear dimension reduction method based on network-based embedding technique.…

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DrImpute
Desktop

DrImpute

Estimates dropout events in scRNA-seq data. DrImpute is a simple, fast hot deck…

Estimates dropout events in scRNA-seq data. DrImpute is a simple, fast hot deck imputation approach. It identifies similar cells based on clustering, and imputation is performed by averaging the…

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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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DropEst
Desktop

DropEst

Performs initial pre-processing and analysis of the droplet-based scRNA-seq…

Performs initial pre-processing and analysis of the droplet-based scRNA-seq data. DropEst in composed of three steps: (1) identifier parsing phase; (2) read mapping phase; and (3) filtering and…

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scPipe
Desktop

scPipe

Addresses the lack of a comprehensive workflow for processing sequencing data…

Addresses the lack of a comprehensive workflow for processing sequencing data from 3 prime end protocols. scPipe can deal with both unique molecular identifiers (UMIs) and sample barcodes, map reads…

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DCSS
Desktop

DCSS Deterministic Column Subset Selection

Provides an application of a thresholding scheme. DCSS is an algorithm to…

Provides an application of a thresholding scheme. DCSS is an algorithm to select informative features, control quality and technical variability. This method has many advantages like the sensitivity…

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VAMF
Desktop

VAMF Varying-censoring Aware Matrix Factorization

Allows to model cell-specific detection patterns using random effects. VAMF…

Allows to model cell-specific detection patterns using random effects. VAMF helps users to identify the factors in the case of systematic bias. This tool represents a probabilistic dimension…

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IA-SVA
Desktop

IA-SVA Iteratively Adjusted Surrogate Variable Analysis

Identifies multiple and potentially correlated hidden sources of variation from…

Identifies multiple and potentially correlated hidden sources of variation from scRNA-Seq data. IA-SVA is capable of high statistical power and low error rate and delivers marker genes associated…

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AUCell
Desktop

AUCell Area Under a Cell

Identifies cells with active gene regulatory networks (GRNs) in single cell…

Identifies cells with active gene regulatory networks (GRNs) in single cell RNA-seq data. AUCell calculates the enrichment of the regulon as an area under the recovery curve (AUC) across the ranking…

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SCENIC
Desktop

SCENIC Single Cell rEgulatory Network Inference and Clustering

Allows to reconstruct gene regulatory networks (GRNs). SCENIC uses single-cell…

Allows to reconstruct gene regulatory networks (GRNs). SCENIC uses single-cell RNA-seq data to identify stable cell states. It analyzes all the co-expression modules using cis-regulatory motif…

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UNCURL
Desktop

UNCURL UNified CompUtational framework for scRNA-seq data processing and Learning

Allows unsupervised and semi-supervised learning using Single Cell RNA-Seq…

Allows unsupervised and semi-supervised learning using Single Cell RNA-Seq data. To operate these learning, UNCURL provides a method for standardizing any prior biological information including bulk…

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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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Topslam
Desktop

Topslam Topologically aware Simultaneous Localisation And Mapping

Allows to estimate the origin of the epigenetic/Waddington landscape which…

Allows to estimate the origin of the epigenetic/Waddington landscape which underlies a population of individual cells. Topslam provides a method for using high resolution single cell transcription…

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SAVER
Desktop

SAVER Single-cell Analysis Via Expression Recovery

Recovers the true expression level of each gene in each cell. SAVER is based on…

Recovers the true expression level of each gene in each cell. SAVER is based on adaptive shrinkage to a multi-gene prediction model. It removes technical variation while retaining biological…

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scTDA
Desktop

scTDA single-cell Topological Data Analysis

Serves for topology-based computational analyses. scTDA realizes temporal…

Serves for topology-based computational analyses. scTDA realizes temporal studies and unbiased transcriptional regulation studies. It is an unsupervised statistical framework that can characterize…

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InformationMeas…
Desktop

InformationMeasures

Estimates multivariate information (MVI) measures. InformationMeasures is a…

Estimates multivariate information (MVI) measures. InformationMeasures is a package which supports information measures such as entropy, mutual information (MI), conditional mutual information (CMI)…

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Neural network…
Web

Neural network based cell type retrieval

Allows analysis and retrieval of single cell RNA-Seq data. Neural network based…

Allows analysis and retrieval of single cell RNA-Seq data. Neural network based cell type retrieval is based on neural networks (NN) to obtain a reduced dimension representation of the single cell…

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CellView
Web

CellView

Provides easy and intuitive exploration of single cell transcriptome data.…

Provides easy and intuitive exploration of single cell transcriptome data. CellView allows knowledge-based and hypothesis-driven exploration of processed single cell transcriptomic data. It can…

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UBiT2
Web
Desktop

UBiT2 User-friendly BioInformatics Tools

Provides installation-free, offline alignment, analysis, and visualization of…

Provides installation-free, offline alignment, analysis, and visualization of RNA-sequencing as well as qPCR data. UBiT2 can perform gene set enrichment testing by using the non-parametric minimal…

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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…

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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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WemIQ
Desktop
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BTR
Desktop

BTR BoolTraineR

Reconstructs and trains asynchronous Boolean models using single-cell…

Reconstructs and trains asynchronous Boolean models using single-cell expression data. BTR is a model learning algorithm that can infer both network structure and Boolean rules without needing…

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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…

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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…

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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…

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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…

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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,…

ROMA
Desktop

ROMA Representation Of Module Activity

Approximates the expression data of a gene set by its first principal…

Approximates the expression data of a gene set by its first principal component. ROMA is based on the simplest uni-factor linear model of gene regulation. It addresses the issue of quantifying the…

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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…

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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.

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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.…

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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)…

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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…

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UMIS
Desktop

UMIS Unique Molecular IdentifierS

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…

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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…

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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.…

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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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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…

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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…

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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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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…

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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.

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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…

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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…

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SoptSC
Desktop

SoptSC

Provides a computational method for single cell data analysis. SoptSC is a…

Provides a computational method for single cell data analysis. SoptSC is a MATLAB package.

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PBA
Desktop

PBA Population Balance Analysis

Provides a method for population balance analysis. PBA is a python application…

Provides a method for population balance analysis. PBA is a python application that allows computation of possible dynamical trajectories and their associated properties. It authorizes to calculate a…

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NetworkInferenc…
Desktop

NetworkInference

Allows users to deduce undirected networks. NetworkInference is a standalone…

Allows users to deduce undirected networks. NetworkInference is a standalone software which implements four algorithms for providing a fully connected, weighted network with indication about edge’s…

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dropSeqPipe
Desktop

dropSeqPipe

Allows users to transform raw data from dropSeq/scrbSeq experiment to the final…

Allows users to transform raw data from dropSeq/scrbSeq experiment to the final count matrix with QC plots. dropSeqPipe is an open source application that can perform five different tasks: (i)…

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demuxlet
Desktop

demuxlet

Provides a method for deconvoluting sample identity. demuxlet is a standalone…

Provides a method for deconvoluting sample identity. demuxlet is a standalone software that can be run with multiple barcoded single cell RNA-seq options. It also permits to detect multiplets among…

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badger
Desktop

badger

Allows users to investigate single-cell RNA-seq data for detecting copy number…

Allows users to investigate single-cell RNA-seq data for detecting copy number alterations and loss of heterozygosity events. badger is a R package which provides a set of statistical methods based…

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Anchor
Desktop

Anchor

Offers an application for detecting unimodal, bimodal, and multimodal…

Offers an application for detecting unimodal, bimodal, and multimodal characteristics. Anchor is a python package which can analyze normalized binary data.

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SingleCellExper…
Desktop

SingleCellExperiment

Defines a S4 class for storing data from single-cell experiments.…

Defines a S4 class for storing data from single-cell experiments. SingleCellExperiment is an R package that includes specialized methods to store and retrieve spike-in information, dimensionality…

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MCXpress
Desktop

MCXpress

Analyses RNA-seq data using an approach based on Multiple Correspondence…

Analyses RNA-seq data using an approach based on Multiple Correspondence Analysis (MCA). MCA is a dimensionality reduction technique that allows the representation of both individuals (cells) and…

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Bonvoyage
Desktop

Bonvoyage

Transforms percentage-based units into a 2d space to evaluate changes in…

Transforms percentage-based units into a 2d space to evaluate changes in distribution with both magnitude and direction. Bonvoyage is a python package.

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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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PoissonUMIs
Desktop

PoissonUMIs Poisson Modelling of scRNASeq UMI counts

Models single-cell RNASeq data quantified by counting unique molecular…

Models single-cell RNASeq data quantified by counting unique molecular identifiers (UMIs). PoissonUMIs is an R package providing functions for fitting, analyzing and visualizing single-cell RNASeq…

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flotilla
Desktop

flotilla

Visualizes transcriptome (RNA expression) data from hundreds of samples.…

Visualizes transcriptome (RNA expression) data from hundreds of samples. Flotilla is a Python package. Flotilla is an open source, community-driven software written in Python that enables biologists…

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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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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…

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scTCRseq
Desktop

scTCRseq

Allows recovering of T cell receptor (TCR) data. scTCRseq is a pipeline for…

Allows recovering of T cell receptor (TCR) data. scTCRseq is a pipeline for processing single cell RNAseq data.

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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…

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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…

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