Laks/README.md

In junseonghwan/ScRNACloneEvaluation: ScRNA clone evaluation.

Scripts and R code for analyzing data from Laks

Pre-processing

• Merge single cell DLP data to generate pseudo-bulk data.
  • GeneratePseudoBulk.py.
  • MergeBAMs.sh.
• Run copy number analysis. We use TitanCNA.

Extracting data

• Extract exonic SNVs from the SNV data [here](https://zenodo.org/record/3445364/files/ov2295_clone_snvs.csv.gz.
• Get read counts from the pseudo bulk data and generate bulk data.
  • Do this for each region separately for multi-region analysis.
• Extract read counts from single cell RNA-seq data.
• Generate single cell data and single cell hyper parameters.

Data for methods for comparison

• PhyloWGS:
  • Generate VCF file at exonic SNVs from the pseudo-bulk file.
  • Run PhyloWGS' parser that takes the VCF and TitanCNA output to generate the input files.
• Generate single cell data matrices for B-SCITE and ddClone.
  • Custom script.
• Generate data for Canopy:
  • Need to run a separate copy number analysis software?

Scripts for inference

• Our method
• PhyloWGS
• B-SCITE
• ddClone
• Canopy

Scripts for evaluation

• Code written in Python notebook.

junseonghwan/ScRNACloneEvaluation documentation built on Aug. 18, 2020, 8:53 p.m.