BrMPhylo (phylogenetics from bulk RNA-seq data)

https://github.com/CMUSchwartzLab/BrM-Phylo

C3

https://github.com/jackhou2/C3

DawnRank: Discovering Personalized Driver Mutations in Cancer

http://genome.compbio.cs.cmu.edu/~jianma/software/DawnRank/

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

https://github.com/bchidest/DBC

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

https://github.com/zhao-biophotonics/ExPath-reg

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)

https://github.com/ma-compbio/LDGM 

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

http://genome.compbio.cs.cmu.edu/~jianma/software/NCIS

SCS_deconvolution (joint bulk and single-cell CNA deconvolution)

https://github.com/CMUSchwartzLab/SCS_deconvolution 

TUSV (tumor phylogenetics incorporating CNA and SV markers)

https://github.com/jaebird123/tusv

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

https://github.com/ma-compbio/Weaver