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.
☆44Apr 18, 2024Updated 2 years ago
Alternatives and similar repositories for pairtree
Users that are interested in pairtree are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Fast method for inferring cancer clonal population structure from SNV data.☆76Jan 20, 2026Updated 9 months ago
- Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation☆27Aug 31, 2026Updated last month
- Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq☆13Apr 2, 2024Updated 2 years ago
- ☆17Aug 11, 2021Updated 5 years ago
- Workflow for Sequenza, cellularity and ploidy☆28Jun 11, 2026Updated 4 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆45Aug 21, 2025Updated last year
- A framework to infer mutational signatures in cancer over time☆58Jul 9, 2019Updated 7 years ago
- Multi-sample cancer phylogeny reconstruction☆36Oct 19, 2017Updated 9 years ago
- ☆19Jan 30, 2023Updated 3 years ago
- ☆12Apr 25, 2024Updated 2 years ago
- This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…☆20Jul 6, 2026Updated 3 months ago
- Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data…☆16Mar 6, 2024Updated 2 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆34Feb 18, 2026Updated 8 months ago
- Analysis pipeline for cancer sequencing data☆112Sep 28, 2026Updated last month
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- A comprehensive toolkit for mutational signature analysis☆44Sep 14, 2026Updated last month
- An R package to time somatic mutations☆71Dec 12, 2020Updated 5 years ago
- HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jo…☆73Sep 29, 2026Updated last month
- Pan gGnome Viewer☆10Sep 24, 2026Updated last month
- Application for inferring subclonal composition and evolution from whole-genome sequencing data.☆114Oct 12, 2022Updated 4 years ago
- ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) is a novel framework for the inference of a set of statistically significant temporal pa…☆12Apr 18, 2025Updated last year
- Structural Variation breakpoint discovery via adaptive learning☆17Jul 6, 2023Updated 3 years ago
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆232Feb 4, 2026Updated 8 months ago
- Git repo for CONIPHER tree building☆27Oct 22, 2026Updated last week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆151Sep 9, 2020Updated 6 years ago
- Battenberg R package for subclonal copynumber estimation☆100May 11, 2026Updated 5 months ago
- dN/dS methods to quantify selection in cancer and somatic evolution☆243Aug 25, 2026Updated 2 months ago
- commandline manipulation of genomic variants and NGS reads☆20Oct 19, 2026Updated last week
- Model-based tumour subclonal deconvolution using population genetics☆36Dec 2, 2025Updated 10 months ago
- Provide programmatic access to the tonsil cell atlas datasets☆10Oct 22, 2026Updated last week
- R wrapper for utilizing the SigProfilerMatrixGenerator framework☆20Jan 29, 2026Updated 9 months ago
- Python function for TMB snake plots☆16Feb 12, 2026Updated 8 months ago
- Somatic point mutation caller☆35Jan 7, 2026Updated 9 months ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity…☆23Jan 17, 2025Updated last year
- Single-Cell Genotyping Tool☆218Updated this week
- ASCAT R package☆205Feb 12, 2026Updated 8 months ago
- Evolutionary frequency visualization tool of temporal data☆24Jan 25, 2022Updated 4 years ago
- Precision HLA typing from next-generation sequencing data☆225May 20, 2026Updated 5 months ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆53May 20, 2022Updated 4 years ago
- Differential Mutation Analysis☆11May 24, 2020Updated 6 years ago