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.

Installation

To install fastCNV, run in R:

remotes::install_github("must-bioinfo/fastCNV")

Usage

Extensive tutorials to run fastCNVon 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 :