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:
- Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation☆27Updated this week
- Fast method for inferring cancer clonal population structure from SNV data.☆77Jan 20, 2026Updated 7 months ago
- A framework to infer mutational signatures in cancer over time☆58Jul 9, 2019Updated 7 years ago
- A comprehensive toolkit for mutational signature analysis☆42Jul 19, 2024Updated 2 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆34Feb 18, 2026Updated 6 months ago
- 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.
- Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq☆13Apr 2, 2024Updated 2 years ago
- Structural Variation breakpoint discovery via adaptive learning☆17Jul 6, 2023Updated 3 years ago
- Pan gGnome Viewer☆10Jul 10, 2025Updated last year
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆44Aug 21, 2025Updated last year
- Somatic point mutation caller☆34Jan 7, 2026Updated 7 months ago
- Workflow for Sequenza, cellularity and ploidy☆28Jun 11, 2026Updated 2 months ago
- Model-based tumour subclonal deconvolution using population genetics☆36Dec 2, 2025Updated 8 months ago
- ☆11Apr 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 last month
- 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.
- R package to organise and standardise your genomic variant calls obtained with different callers.☆11Jul 15, 2019Updated 7 years ago
- ☆18Jan 30, 2023Updated 3 years ago
- SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity…☆23Jan 17, 2025Updated last year
- Python function for TMB snake plots☆16Feb 12, 2026Updated 6 months ago
- Filters for Next Generation Sequencing☆13Oct 31, 2024Updated last year
- Differential Mutation Analysis☆11May 24, 2020Updated 6 years ago
- Analysis pipeline for cancer sequencing data☆112Apr 24, 2026Updated 4 months ago
- Battenberg R package for subclonal copynumber estimation☆100May 11, 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
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Python package for cancer early detection based on a model of cancer evolution and circulating tumor DNA (ctDNA) shedding☆13Jan 8, 2021Updated 5 years 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
- Allele-Specific Quantification of Structural Variations in Cancer Genomes☆19Mar 5, 2019Updated 7 years ago
- Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data☆20Mar 18, 2023Updated 3 years ago
- An R package to time somatic mutations☆73Dec 12, 2020Updated 5 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆103Jul 24, 2026Updated last month
- ☆15Apr 20, 2023Updated 3 years ago
- Single-Cell Genotyping Tool☆219Oct 2, 2023Updated 2 years ago
- NGSeminar on the use of Jupyter and R notebooks in biomedical research☆13Jan 28, 2023Updated 3 years ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- iLASH - IBD Estimation Using Locality Sensitive Hashing☆18Nov 6, 2025Updated 9 months ago
- DriverPower☆26Jan 18, 2025Updated last year
- Evolutionary frequency visualization tool of temporal data☆24Jan 25, 2022Updated 4 years ago
- Summary of a single or multiple MAF files.☆14Feb 5, 2025Updated last year
- R implementation of the Reshef and Rumker CNA method (https://github.com/immunogenomics/cna)☆15Aug 10, 2026Updated 2 weeks ago
- ☆11May 26, 2023Updated 3 years ago
- ☆13Apr 16, 2026Updated 4 months ago