CNViz
CNViz takes probe, gene, and segment-level log2 copy number ratios and launches a Shiny app to visualize your sample's copy number profile. You can also integrate loss of heterozygosity (LOH) and single nucleotide variant (SNV) data.
- Bioconductor
- https://bioconductor.org/packages/CNViz
Source attribution
- Bioconductor — CNViz
Related resources
CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data.
CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines.
Uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers.
karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.
Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.