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. 

Code

SlideCNA_0.1.0.zip: SlideCNA code

SlideCNA_Analysis.zip: Analysis code

Raw data to prepare input to SlideCNA (txt format):

HTAPP-895-SMP-7359_slide-seq_beads.txt: Slide-seq bead metadata (as input for RCTD)

HTAPP-895-SMP-7359_slide-seq_coords.txt: Slide-seq bead spatial coordinates (pos_x, pos_y) (as input for RCTD)

HTAPP-895-SMP-7359_scRNA-seq_counts.txt: matching scRNA-seq counts (as input for RCTD and direct input for SlideCNA on non-spatial data)

HTAPP-895-SMP-7359_scRNA-seq_cell_types.txt: scRNA-seq cell type annotations (as input for RCTD)

HTAPP-895-SMP-7359_scRNA-seq_cells_df.txt: scRNA-seq cell metadata including cell label, annotation for cluster type (“Malignant”, “Non-malignant”) (as direct input for SlideCNA on non-spatial data)

Prepared data for direct input to SlideCNA (txt format):

HTAPP-895-SMP-7359_slide-seq_beads_annotated.txt: Slide-seq bead metadata including bead label, annotation for cluster type (“Malignant”, “Non-malignant”), and spatial coordinates of each bead (pos_x, pos_y) (as direct input for SlideCNA)

HTAPP-895-SMP-7359_slide-seq_counts.txt: Slide-seq counts (as direct input for SlideCNA)

HTAPP-895-SMP-7359_slide-seq_bs_beads_df.txt: Slide-seq bead metadata after TACCO bead decomposition with split bead label, annotation for cluster type (“Malignant”, “Non-malignant”), and spatial coordinates of each split bead (pos_x, pos_y) (as direct input for SlideCNA)

HTAPP-895-SMP-7359_slide-seq_bs_counts.txt: Slide-seq counts after TACCO bead decomposition (as direct input for SlideCNA)

gene_pos.txt: genomic gene positions along the chromosomes (as direct for input for slideCNA)

Raw data to prepare input to slideCNA starting (h5ad format):

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 (h5ad format):

HTAPP-895-SMP-7359_slide-seq_processed_RCTD.h5ad: slide-seq data with RCTD cell type annotation (as direct input for slideCNA)

HTAPP-895-SMP-7359_slide-seq_processed_bs.h5ad: slide-seq beadsplitting results (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