Entering edit mode
8.6 years ago
Lemire
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940
I am releasing CELLULOID: an R package to evaluate ploidy, cellularity, clonal and sub-clonal copy-number events from tumour whole genome sequencing data, and to derive absolute copy numbers profiles. This was developed at the Ontario Institute for Cancer Research.
Tutorial and installation instructions can be found at https://github.com/mathieu-lemire/celluloid_0.11_tutorial
Features include:
- an ad hoc measurement of the weighted fraction of the tumour genome that is captured by the model, defined by values of ploidy, cellularity and subclonal proportions;
- a global visual assessment of both the tumor copy number profile, in the form of a contour plot, as well as the fitting model, for curation purposes; e.g. https://github.com/mathieu-lemire/celluloid_0.11_tutorial/blob/v0.11.0/Figures/FigureN3.png
- copy-number segment graphs that can be annotated; e.g. https://github.com/mathieu-lemire/celluloid_0.11_tutorial/blob/v0.11.0/Figures/segments_page1.png
Methods are briefly introduced in tutorial files. Manuscript to follow soon in BioRxiv. Feedback is welcome, this is a pre-publication release.
Mathieu
@CELLULOID_R for updates