Introduction
fastCNV
is a package that helps you detect, plot and analyse the putative Copy Number Variations (CNVs) in single cell (scRNA-seq) data or Spatial Transcriptomics (ST) data. Built on SeuratObject
, it is easily integrated into scRNA-seq or ST pipelines.
WARNING: Project is still under construction and function usage may change.
Usage
Extensive tutorials to run fastCNV
on scRNA-seq and spatial transcriptomics data are available to get started here.
NEW : RUN fastCNV ON YOUR VISIUM HD DATA
You can now run fastCNV
on visium HD data using fastCNV_10XHD()
You can also see the cnv clusters on the slide :
And see the clonality tree :
Capabilities
fastCNV
can plot a heatmap of inferred CNVs:
It also calculates a cnv_fraction
, which can be plotted with Seurat
standard plotting functions:
cnv_fractions
can also be visualized spatially for Spatial Transcriptomics samples:
And cnv_fractions
can be used to obtain clonal clusters (cnv_clusters
):
The subclonality tree can be plotted too :