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dpclust

Dirichlet Process based methods for subclonal reconstruction of tumours

magic

MAGIC - imputation and de-noising single-cell RNA seq data sets

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.

mpn-aml-pairtree

mutsim

Framework for generating simulated data with which to evaluate cancer evolutionary history reconstruction methods. Suitable for use with Pairtree, SubMARine, and other methods.

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.

sciclone

An R package for inferring the subclonal architecture of tumors

scprep

A collection of scripts and tools for loading, processing, and handling single cell data.