This repo contains commented notebooks to illustrate the usage of the scGate package
A DEMO for the basic functionalities of scGate: scGate basics
For scGate installation instructions refer to the scGate repository
We will be posting here several demos for scGate usage in different scenarios:
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A demo of the basic functionalities of scGate on scRNA-seq data - scGate basics
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Purifying cells on multi-modal scATAC-seq + scRNA-seq data - scGate ATAC+RNA
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Purifying cells on CITE-seq data - scGate CITE-seq
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scGate to annotate scRNA-seq datasets integrated with Harmony and STACAS - scGate integrated
To access the raw code and run these demos on your machine, you may also clone the repository:
git clone https://github.com/carmonalab/scGate.demo.git
Then open the project scGate.demo.Rproj in Rstudio and follow the commands in one of the available notebooks.