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Read count simulation software tools | Single-cell RNA sequencing data analysis

A common way to test the performance of an analysis method is through a simulation. Simulated data provides a known truth to test against, making it possible to see whether a method has been implemented correctly, whether the assumptions of the…
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Splatter
Desktop

Splatter

Offers a simple interface for creating complex simulations that are…

Offers a simple interface for creating complex simulations that are reproducible and well-documented. Splatter is an R package for reproducible and accurate simulation of single-cell RNA sequencing…

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Linnorm
Desktop

Linnorm

Provides a linear model and normality based transformation method. Linnorm is…

Provides a linear model and normality based transformation method. Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIPseq count data or any large-scale count data. It transforms such…

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powsimR
Desktop

powsimR

Simulates and evaluates differential expression from bulk and especially…

Simulates and evaluates differential expression from bulk and especially single-cell RNA-seq data. powsimR can not only estimate sample sizes necessary to achieve a certain power, but also informs…

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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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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…

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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…

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BASiCS
Desktop

BASiCS Bayesian Analysis of Single-Cell Sequencing data

Provides an integrated normalisation method where cell-specific normalising…

Provides an integrated normalisation method where cell-specific normalising constants are estimated as model parameters. BASiCS is an integrated Bayesian hierarchical model where: (i) cell-specific…

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