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BrMPhylo (phylogenetics from bulk RNA-seq data)

C3

DawnRank: Discovering Personalized Driver Mutations in Cancer

Discrimantive Bag-of-Cells (DBC) (machine learning tool for predicting artibtrary cellular images)

ExPath-reg (image registration software for aligning expanded and unexpanded Expansion Pathology (ExPath))

FISHtrees (FISH-based tumor phylogenetics)

ftp://ftp.ncbi.nih.gov/pub/FISHtrees

LDGM (estimate the differential gene regulatory network between two biological conditions such as tumor subtypes)

NCIS (A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression)

SCS_deconvolution (joint bulk and single-cell CNA deconvolution)

TUSV (tumor phylogenetics incorporating CNA and SV markers)

Weaver (returns allele-specific copy numbers of regions and phased breakpoints of structural variants)