nowellpack is a Blang library for cancer genomics. The main current features focus on Bayesian phylogenetic tree inference from single cell data. We make the approximation that change points in the copy number profiles are perfect phylogeny markers. However those markers are observed in a noisy fashion hence the name we give to this model: corrupt phylogenies.
Run an end-to-end pipeline (sampling, summarizing posterior, viz) with:
git clone --depth=1 https://github.com/UBC-Stat-ML/corrupt-nextflow.git
cd corrupt-nextflow
./nextflow run main.nf -resume --tipInclusionProbabilities DATA.csv
Change DATA.csv into the data you are interested in (more below). Provided you have Oracle Java 8 in your PATH variable this will create a directory called deliverables/main containing an inferred tree and a bunch of other outputs.
The input for all included phylogenetic inference methods is a csv file with the following header:
cells,loci,tipInclusionProbabilities
followed by lines of the form
myfirstcell,somelocus,1
...
Note that for the binary model, tipInclusionProbabilities are set to 0 and 1, and a false positive/false negative rates model is inferred jointly.
The loci should follow the format 1_100500001_101000000 where
1 here is the chromosome index, 100500001 is the left boundary of the bin, and 101000000 is the right boundary, both inclusive.
Cells can use arbitrary unique identifiers.