Monocle 3

An analysis toolkit for single-cell RNA-seq.

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Build single-cell trajectories with the software that introduced pseudotime. Find cell fate decisions and the genes regulated as they're made.

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Group and classify your cells based on gene expression. Identify new cell types and states and the genes that distinguish them.

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Differential expression

Find genes that vary between cell types and states, over trajectories, or in response to perturbations using statistically robust, flexible differential analysis.

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Classify and count cells.

Single-cell RNA-Seq experiments allow you to discover (and possibly rare) subtypes of cells. Monocle 3 helps you identify them.

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Identify new marker genes.

Many researchers are using single-cell RNA-Seq to discover new cell types. Monocle 3 can help you purify them or characterize them further by identifying key marker genes that you can use in follow up experiments such as immunofluorescence or flow sorting.

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Robustly track changes over (pseudo) time.

In development, disease, and throughout life, cells transition from one state to another. Monocle introduced the concept of pseudotime, which is a measure of how far a cell has moved through biological progress.

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Dissect cellular decisions with branch analysis.

Single-cell trajectory analysis how cells choose between one of several possible end states. The new reconstruction algorithms introduced in Monocle 3 can robustly reveal branching trajectories, along with the genes that cells use to navigate these decisions.

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