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README.md

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# SCWorkflow
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[![Gitflow Action for R Package Development](https://github.com/NIDAP-Community/SCWorkflow/actions/workflows/gitflow-R-action.yml/badge.svg)](https://github.com/NIDAP-Community/SCWorkflow/actions/workflows/gitflow-R-action.yml)
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[![Version](https://img.shields.io/github/v/release/nidap-community/scworkflow)](https://github.com/NIDAP-Community/SCWorkflow/releases/latest)
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[![Docker Image Version](https://img.shields.io/docker/v/nciccbr/scworkflow?label=docker)](https://hub.docker.com/r/nciccbr/scworkflow)
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[![](https://raw.githubusercontent.com/NIDAP-Community/SCWorkflow/GalaxyCLI/vignettes/SCWorkflow.png)](https://raw.githubusercontent.com/NIDAP-Community/SCWorkflow/GalaxyCLI/vignettes/SCWorkflow.pdf)
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[![](https://raw.githubusercontent.com/NIDAP-Community/SCWorkflow/GalaxyCLI/vignettes/SCWorkflow.png)](https://lucid.app/lucidchart/c7b852ad-72dc-4821-90d5-e45bed0c4199/view)
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<center>**Click Figure to Navigate Workflow**.</center>
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The Single Cell Workflow streamlines the analysis of multimodal Single Cell RNA-Seq data produced from 10x Genomics. It can be run in a docker container, and for biologists, in user-friendly web-based interactive notebooks (NIDAP, Palantir Foundry). Much of it is based on the Seurat workflow in Bioconductor, and supports CITE-Seq data. It incorporates a cell identification step (ModScore) that utilizes module scores obtained from Seurat and also includes Harmony for batch correction.
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For further documentation see our detailed [Docs Website](https://nidap-community.github.io/SCWorkflow/)
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## Install Package
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