Analytic Module Versions

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Model-based Analysis for ChIP-Sequencing (MACS)

The MACS module in ArrayStudio is implemented based on MACS2 beta version MACS2-2.0.10.07032012 (for pair-end data loading) and MACS 1.4.2 (most other parts), which could be different from the original MACS publication.

DESeq2

The DESeq2 module in ArrayStudio is implemented based on DESeq2 v1.10.1.

Voom

The Voom module directly uses the R packages.

For local runs, version number can be found from the "Tools => R Integration => Setup R Script Engine" menu.

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For server runs, version number can be found from the "Manage => Manage R Script Engine" menu (only admins can access this menu).

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Rtsne

The Rtsne module directly uses the R packages: Stochastic Neighbor Embedding using a Barnes-Hut Implementation.

For local runs, version number can be found from the "Tools => R Integration => Setup R Script Engine" menu.

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User should install the rtsne package in the R integrated with ArrayStudio (like this R.exe defined by REngine Excutable Path), run install.packages("Rtsne") in R

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And user can check the option for rtsne to update it, which will make rtsne ready.

For server runs, version number can be found from the "Manage => Manage R Script Engine" menu (only admins can access this menu).

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