Calls Copy Number Alterations from Slide-Seq Data

[Up] [Top]

Documentation for package ‘SlideCNA’ version 0.1.0

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