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Sub-population detection

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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…

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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…

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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…

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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…

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FVFC
Algorithm

FVFC Functional Virtual Flow Cytometry

Intends to identify distribution patterns in cell populations thanks to…

Intends to identify distribution patterns in cell populations thanks to single-cell transcriptome study. FVFC uses gene coexpression network analysis (GCNA) to detect modules of genes with similar…

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SAFE-clustering
Desktop

SAFE-clustering Single-cell Aggregated (From Ensemble) Clustering

Provides stable and robust clustering for scRNA-seq data. SAFE-clustering is an…

Provides stable and robust clustering for scRNA-seq data. SAFE-clustering is an unsupervised ensemble method that: (i) performs independent clustering using four state-of-the-art methods, SC3, CIDR,…

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SAIC
Desktop

SAIC Single cell RNA-seq analysis with iterative clustering

Detects the optimal set of signature genes to separate single cells into…

Detects the optimal set of signature genes to separate single cells into distinct groups. SAIC uses an iterative k-means clustering approach to perform an exhaustive search for the best signature…

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DIMM-SC
Desktop
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scmap
Web
Desktop

scmap

Allows to make unsupervised projection of single cells from an scRNA-seq…

Allows to make unsupervised projection of single cells from an scRNA-seq experiment. scmap is easy to combine with other computational scRNA-seq methods. It is very fast, using 1,000 features taking…

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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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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,…

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SCENT
Desktop

SCENT Single Cell ENTropy

Identifies known cell subpopulations of varying potency, enabling…

Identifies known cell subpopulations of varying potency, enabling reconstruction of cell-lineage trajectories. SCENT is an algorithm that can be used to identify and quantify biologically relevant…

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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…

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