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README.md

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# SCWorkflow
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Workflow Package for Analysis of Single Cell Data
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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)
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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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Some of the steps in the workflow:

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