ethanumn's repositories
mutsim
Framework for generating simulated data with which to evaluate cancer evolutionary history reconstruction methods. Suitable for use with Pairtree, SubMARine, and other methods.
scarlet
SCARLET (Single-cell Algorithm for Reconstructing Loss-supported Evolution of Tumors) is an algorithm that reconstructs tumor phylogenies from single-cell DNA sequencing data. SCARLET uses a loss-supported model that constrains mutation losses based on observed copy-number data.
sciclone
An R package for inferring the subclonal architecture of tumors
dpclust
Dirichlet Process based methods for subclonal reconstruction of tumours
pairtree
Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on scaling to many more cancer samples and cancer cell subpopulations than other algorithms, and on producing concise and informative interactive characterizations of posterior uncertainty.
markdown_readme
Markdown - you can mark up titles, lists, tables, etc., in a much cleaner, readable and accurate way if you do it with HTML.
magic
MAGIC - imputation and de-noising single-cell RNA seq data sets
scprep
A collection of scripts and tools for loading, processing, and handling single cell data.