inst/www/helpfiles/add_to_current_analysis.md

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Additional feature layer on the same cells

It is sometimes interesting to appreciate the same data from multiple angles.

One might want to use 50kbp genomic bins for a comprehensive dimensionality reduction and clustering, then run differential analysis using genebodies.

Or using different size of bins and peaks while being able to visualize the different UMAPs on the same cells.

For genetically alterated biological samples one might also count reads at the cytoband level to see if 'de-zooming' still allows to separate cells (see ?ChromSCape::calculate_CNA()).

When ticking this checkbox, data will be added to the current analysis. The data you wish to upload must contain the same cells (e.g. cell barcodes) than the current analysis.

The additional data layers you upload will be kept in alternative slots (see ?SingleCellExperiment::altExp()). You can switch at any time between the different features you counted your data by clicking on 'Features' in the upper bar of the application.

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.