Alternatives and similar repositories for TRONCO

Users that are interested in TRONCO are comparing it to the libraries listed below

• caravagnalab / revolver

  View on GitHub
  Tumour stratification by maximum-likelihood repeated evolution from multi-region sequencing data
  ☆67Dec 25, 2022Updated 3 years ago
• amf71 / cloneMap

  View on GitHub
  An R package to plot maps of clone distributions in somatic evolution
  ☆19Jan 8, 2024Updated 2 years ago
• marcjwilliams1 / neutralitytestr

  View on GitHub
  Testing a neutral evolution model on cancer sequencing data
  ☆10Feb 17, 2021Updated 4 years ago
• marcjwilliams1 / SubClonalSelection.jl

  View on GitHub
  Inferring selection in cancer sequencing data using ABC and population based simulations
  ☆11Jan 31, 2021Updated 5 years ago
• hdng / clonevol

  View on GitHub
  Inferring and visualizing clonal evolution in multi-sample cancer sequencing
  ☆150Sep 9, 2020Updated 5 years ago
• caravagnalab / mobster

  View on GitHub
  Model-based tumour subclonal deconvolution using population genetics
  ☆34Dec 2, 2025Updated 2 months ago
• vanallenlab / facets

  View on GitHub
  Implementation of FACETS for Terra
  ☆12Jan 20, 2023Updated 3 years ago
• CompEpigen / ezASCAT

  View on GitHub
  Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R
  ☆12Dec 6, 2021Updated 4 years ago
• beroukhim-lab / BISCUT-py3

  View on GitHub
  ☆11Apr 25, 2024Updated last year
• Wedge-lab / battenberg

  View on GitHub
  Battenberg R package for subclonal copynumber estimation
  ☆95Updated this week
• raphael-group / calder

  View on GitHub
  CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk …
  ☆15Nov 28, 2023Updated 2 years ago
• VanLoo-lab / ascat

  View on GitHub
  ASCAT R package
  ☆199Updated this week
• cancersysbio / SCIMET

  View on GitHub
  Spatial Computational Inference of MEtastatic Timing (SCIMET)
  ☆14May 28, 2019Updated 6 years ago
• DecodeGenetics / read_haps

  View on GitHub
  Detects human contamination in bam files
  ☆16Sep 10, 2020Updated 5 years ago
• lilit-nersisyan / computel

  View on GitHub
  Compute mean telomere length from Whole Genome Sequencing data.
  ☆15Feb 15, 2024Updated 2 years ago
• beroukhim-lab / ascets

  View on GitHub
  This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…
  ☆18Jan 31, 2024Updated 2 years ago
• mskcc / facets

  View on GitHub
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆158Jan 29, 2026Updated 2 weeks ago
• gavinha / TitanCNA

  View on GitHub
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆100Apr 20, 2021Updated 4 years ago
• NKI-CCB / DISCOVER

  View on GitHub
  DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data
  ☆32May 1, 2025Updated 9 months ago
• cgab-ncc / FIREVAT

  View on GitHub
  FInding REliable Variants without ArTifacts
  ☆23Nov 18, 2022Updated 3 years ago
• stjude / cis-x

  View on GitHub
  Search for activating regulatory variants in the tumor genome
  ☆14Apr 11, 2025Updated 10 months ago
• mskcc / mimsi

  View on GitHub
  Microsatellite Instability Classification using Multiple Instance Learning
  ☆27Mar 3, 2025Updated 11 months ago
• mskilab-org / fishHook

  View on GitHub
  R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after cor…
  ☆32Oct 29, 2025Updated 3 months ago
• raerose01 / deconstructSigs

  View on GitHub
  deconstructSigs
  ☆144Apr 24, 2023Updated 2 years ago
• jrflab / modules

  View on GitHub
  MSKCC Reis-Filho Lab pipeline thingy
  ☆18Jan 18, 2026Updated 3 weeks ago
• raphael-group / wext

  View on GitHub
  A Weighted Exact Test for Mutually Exclusive Mutations in Cancer
  ☆21Sep 30, 2018Updated 7 years ago
• morrislab / TrackSig

  View on GitHub
  A framework to infer mutational signatures in cancer over time
  ☆56Jul 9, 2019Updated 6 years ago
• pughlab / bamgineer

  View on GitHub
  Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
  ☆38Jul 30, 2020Updated 5 years ago
• aaronmck / SC_GESTALT

  View on GitHub
  GESTALT processing pipeline for barcodes captured with single-cell RNA sequencing
  ☆13Jan 26, 2020Updated 6 years ago
• raphael-group / machina

  View on GitHub
  Framework for Metastatic And Clonal History INtegrative Analysis
  ☆36Mar 5, 2021Updated 4 years ago
• parklab / MuSiCal

  View on GitHub
  A comprehensive toolkit for mutational signature analysis
  ☆41Jul 19, 2024Updated last year
• PoisonAlien / somaticfreq

  View on GitHub
  knowledge-based genotyping of cancer hotspots from the tumor BAM files
  ☆21Dec 14, 2021Updated 4 years ago
• ShixiangWang / DoAbsolute

  View on GitHub
  Automate Absolute Copy Number Calling using 'ABSOLUTE' package
  ☆41Nov 28, 2023Updated 2 years ago
• im3sanger / dndscv

  View on GitHub
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆231May 15, 2025Updated 9 months ago
• caravagnalab / CNAqc

  View on GitHub
  Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation
  ☆25Jan 28, 2026Updated 2 weeks ago
• raredd / kmdata

  View on GitHub
  kmdata: A Database of Reconstructed Individual Patient Level Data from 153 Oncology Clinical Trials
  ☆15May 27, 2025Updated 8 months ago
• abcdbug / dbug

  View on GitHub
  notes and materials from dbug meetings
  ☆10Sep 26, 2018Updated 7 years ago
• mskilab-org / gUtils

  View on GitHub
  Utility functions to extend and optimize GenomicRanges functionality.
  ☆10Mar 6, 2025Updated 11 months ago
• jni / jax-workshop

  View on GitHub
  ☆13Jul 18, 2019Updated 6 years ago