SlideCNA example data

This repository contains the data necessary to follow the slideCNA vignettes showcasing possible avenues of copy number aberration (CNA) calling in slide-seq data. Raw data to prepare input to slideCNA starting: HTAPP-895-SMP-7359_scRNAseq_processed.h5ad: annotated scRNAseq reference data for annotation transfer (input for slide-seq cell type annotation with RCTD and beadsplitting) HTAPP-895-SMP-7359_slide_seq_processed.h5ad: cleaned slide-seq unannotated raw data (input for slide-seq cell type annotation with RCTD and beadsplitting) Prepared data for direct input to slideCNA: HTAPP-895-SMP-7359_slide-seq_processed_bs.h5ad: slide-seq beadsplitting results (as direct input for slideCNA) HTAPP-895-SMP-7359_slide-seq_processed_RCTD.h5ad: slide-seq data with RCTD cell type annotation (as direct input for slideCNA) gene_pos.Robj: genomic gene positions along the chromosomes (input for slideCNA) CNA profiles to calculate correlations between different method-data combinations: HTAPP-878-SMP-7149_correlation.tar.gz HTAPP-880-SMP-7179_correlation.tar.gz HTAPP-895-SMP-7359_correlation.tar.gz HTAPP-944-SMP-7479_correlation.tar.gz