R: Calls Copy Number Alterations from Slide-Seq Data

# Calls Copy Number Alterations from Slide-Seq Data

## Documentation for package ‘SlideCNA’ version 0.1.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

bin | Subfunction of bin_metadata() for expression/positional binning
bin_metadata | Spatio-molecular binning of relative expression intensities
center_rm | Center expression intensities
clone_so | Add clone information to meta data of seurat object and bin the beads
cnv_heatmap | Plot CNV scores on a heat map
dat_to_long | Convert data to long format and add in metadata
find_cluster_markers | Find and plot top n DEGs per cluster
find_go_terms | Find and plot top n GO-enriched terms per cluster
get_num_clust | Find optimal number of clusters
long_to_bin | Convert to wide bin x genes + metadata format
make_seurat_annot | Creation of Seurat object
make_so_bin | Make a binned version of a Seurat object
mean_cnv_plot | Plot mean CNV scores per bin and per chromosome
mode | Subfunction of long_to_bin() that finds mode of vector/column
plot_clones | Plot cluster/clone information
prep | Infercnv-based preparation of relative gene expression intensities
prep_cnv_dat | Prepare data for CNV heat map
quantile_plot | Plot CNV score quantiles per bin and per chromosome
ref_adj | Adjust for Reference (Normal) Beads
run_enrichr | Subfunction to get significantly enriched GO terms given a set of signfiicant beads and genes
run_slide_cna | Run SlideCNA workflow
scalefit | Subfunction for scale_nUMI that normalizes a given bin for UMI count and centers the mean CNV score at 1
scale_nUMI | Scale for nUMI (UMI Count) to generate CNV scores
SpatialPlot | Spatial plots of meta data
weight_rollmean | Expressional smoothing along a chromosome using a weighted pyramidal moving average
weight_rollmean_sub | Subfunction of weight_rollmean