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Cell lineage and pseudotime inference software tools | Single-cell RNA sequencing data analysis

Inference of lineage structure has been referred to as “pseudotemporal reconstruction” and it can help us understand how cells change state and how cell fate decisions are made (Bendall et al., 2014; Campbell et al., 2015; Trapnell et…
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Wishbone
Desktop

Wishbone

Aligns single cells from differentiation systems with bifurcating branches.…

Aligns single cells from differentiation systems with bifurcating branches. Wishbone pinpoints bifurcation points and labels each cell as pre-bifurcation or as one of two post-bifurcation cell fates…

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Monocle
Desktop

Monocle

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

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

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Seurat
Desktop

Seurat

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

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

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Cycler
Desktop

Cycler

Constructs a continuous trajectory of cell-cycle progression from images of…

Constructs a continuous trajectory of cell-cycle progression from images of fixed cells. Cycler can be used to quantify multiple sources of cell-to-cell variability in mammalian cells permits a…

DPT
Desktop

DPT Diffusion PseudoTime

Measures progression through branching lineages using a random-walk-based…

Measures progression through branching lineages using a random-walk-based distance in diffusion map space. DPT allows for branching and pseudotime analysis on large-scale RNA-seq data sets. This…

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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…

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DeLorean
Desktop

DeLorean

Models time series accounting for noise in the temporal dimension. This R…

Models time series accounting for noise in the temporal dimension. This R package implements the DeLorean model to estimate pseudotimes for cell expression data. The DeLorean model uses a Gaussian…

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Mpath
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Mpath

Resolves multi-branching single-cell developmental trajectories, allowing for…

Resolves multi-branching single-cell developmental trajectories, allowing for multiple cell fates stemming from a single progenitor cell type. Mpath is an algorithm able to predict individual cell’s…

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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…

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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…

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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…

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Phenopath
Desktop

Phenopath

Provides a contribution to the pre-existing arsenal of pseudo-temporal analysis…

Provides a contribution to the pre-existing arsenal of pseudo-temporal analysis algorithms developed across a range of application areas including single cell omics and cancer. PhenoPath generalises…

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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…

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Ouija
Desktop

Ouija

Learns pseudotimes from single-cell RNA-seq data. Ouija is an orthogonal…

Learns pseudotimes from single-cell RNA-seq data. Ouija is an orthogonal approach implemented in a latent variable model statistical framework. The software can integrate prior expectations of gene…

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single-cell…
Desktop

single-cell diffusion map

Analyzes single-cell differentiation data. single-cell diffusion map aims to…

Analyzes single-cell differentiation data. single-cell diffusion map aims to deal with the problem of defining differentiation trajectories. Diffusion map are appropriate for the dimension-reduction…

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GrandPrix
Desktop

GrandPrix

Allows users to predict a number of latent dimensions. GrandPrix assists users…

Allows users to predict a number of latent dimensions. GrandPrix assists users in analyzing the single-cell data. This permits researchers to examine the temporal dynamics of complex biological…

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GPseudoRank
Desktop

GPseudoRank

Provides a Gaussian process latent variable model for pseudotemporal ordering.…

Provides a Gaussian process latent variable model for pseudotemporal ordering. GPseudoRank is a fully Bayesian pseudotime method to sample from a posterior distribution of permutations rather than…

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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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MFA
Desktop

MFA Mixtures of Factor Analysers

Provides probabilistic inference of single-cell bifurcations. MFA is an R…

Provides probabilistic inference of single-cell bifurcations. MFA is an R package implementing Gibbs sampling for a Bayesian hierarchical mixture of factor analyzers for inference of bifurcating…

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FORKS
Desktop

FORKS Finding Orderings Robustly using K-means and Steiner trees

Finds a robust pseudo-temporal ordering of cells with no tuning of…

Finds a robust pseudo-temporal ordering of cells with no tuning of hyperparameters. FORKS is adaptable to both single-cell or bulk differentiation data and does not requires hyper-parameter tuning.…

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TASIC
Desktop

TASIC

Determines temporal trajectories, branching and cell assignments in single cell…

Determines temporal trajectories, branching and cell assignments in single cell time series experiments. Temporal Assignment of SIngle Cells (TASIC) uses on a probabilistic graphical model to…

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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…

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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…

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SCODE
Desktop

SCODE

Infers regulatory networks based on ordinary differential equations (ODEs).…

Infers regulatory networks based on ordinary differential equations (ODEs). SCODE is an algorithm for single-cell RNA-Seq (scRNA-Seq) performed on differentiating cells. The software is based on the…

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switchde
Desktop

switchde

Models differential expression over pseudotime. switchde is a statistical…

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

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slingshot
Desktop

slingshot

Identifies and characterizes continuous developmental trajectories in…

Identifies and characterizes continuous developmental trajectories in single-cell sequencing data. Slingshot is a lineage inference tool that combines stable techniques necessary for noisy…

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SCOUP
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Scorpius
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Scorpius

Infers computational models of linear dynamic processes in an accurate and…

Infers computational models of linear dynamic processes in an accurate and data-driven approach. Scorpius is an R package that enables de novo investigation and characterization of dynamic processes…

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SCIMITAR
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gpseudotime
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gpseudotime

Performs Bayesian inference on the pseudotimes. gpseudotime combines Gaussian…

Performs Bayesian inference on the pseudotimes. gpseudotime combines Gaussian Process Latent Variable Models (GP-LVM) with a electroGP prior. It creates a reduced dimension representation of cells…

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Embeddr
Desktop

Embeddr

Allows pseudotemporal ordering of single-cell RNA-seq. Embeddr employs…

Allows pseudotemporal ordering of single-cell RNA-seq. Embeddr employs non-linear dimensionality reduction of the gene-space using laplacian eigenmaps (also known as spectral embedding) - a manifold…

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pseudogp
Desktop

pseudogp

Fits probabilistic pseudotime trajectories to two-dimensional reduced-dimension…

Fits probabilistic pseudotime trajectories to two-dimensional reduced-dimension representations of genomic data using Bayesian Gaussian Process Latent Variable Models. Pseudogp is an R package that…

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