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aertslab / SCope

Fast visualization tool for large-scale and high dimensional single-cell data
GNU General Public License v3.0
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Compare RNA and ATAC data #242

Open MaybeJustJames opened 4 years ago

MaybeJustJames commented 4 years ago

We have generated multiple scATAC-seq data sets for which scRNA-seq is also available. New methods have appeared to integrate (warp) such data sets, such as Seurat v3 and Liger. We are also using Gradient Boosting machines to perform such integration. Here, we will expand on the Compare Tab in SCope, to allow comparing RNA and ATAC next to each other. In principle, this is already possible, so the main challenge will be to allow for the adjustment of the mapping parameters (e.g., how peaks are mapped to genes) and to explore the mappings provided by different tools. The use of different scales (e.g. having independent selectors for the color scale) should also be taken into account.

MaybeJustJames commented 4 years ago

Requires fleshed out specification.