judithabk6 / clonesigView external linksLinks
☆18Jan 30, 2023Updated 3 years ago
Alternatives and similar repositories for clonesig
Users that are interested in clonesig are comparing it to the libraries listed below
Sorting:
- cDriver R package for finding candidate driver genes in cancers☆18Jan 18, 2018Updated 8 years ago
- ☆11Apr 25, 2024Updated last year
- Testing a neutral evolution model on cancer sequencing data☆10Feb 17, 2021Updated 4 years ago
- Tool for analyzing the inter-mutational distances between SNV-SNV and INDEL-INDEL mutations. Tool separates mutations into clustered and …☆14Updated this week
- DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell frac…☆22May 21, 2024Updated last year
- ☆18May 8, 2023Updated 2 years ago
- Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation☆25Jan 28, 2026Updated 2 weeks ago
- ☆16Aug 11, 2021Updated 4 years ago
- Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors☆34Jan 27, 2026Updated 2 weeks ago
- R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al.…☆16Feb 17, 2021Updated 4 years ago
- DriverPower☆26Jan 18, 2025Updated last year
- Python function for TMB snake plots☆16Aug 6, 2020Updated 5 years ago
- Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data…☆17Mar 6, 2024Updated last year
- An R package for predicting HR deficiency from mutation contexts☆30Feb 13, 2025Updated last year
- Ａ user-friendly Python toolkit, which provides a comprehensive pipeline to easily explore the cohort-based mutational characterization fo…☆21Oct 27, 2022Updated 3 years ago
- NOTE: This package has been renamed to sparrow and will be submitted to Bioconductor 3.14. Please use that package instead. This is kept …☆21Nov 16, 2020Updated 5 years ago
- Codes and Data for FFPEsig manuscript☆17Jan 17, 2024Updated 2 years ago
- A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations☆35Jan 28, 2022Updated 4 years ago
- Subclonal Hierarchy Inference from Somatic Mutations☆21Feb 25, 2025Updated 11 months ago
- Somatic coding and non-coding mutation enrichment analysis for tumor WGS data☆12Jun 16, 2021Updated 4 years ago
- Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data☆11Jul 13, 2020Updated 5 years ago
- R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework☆41Jan 28, 2026Updated 2 weeks ago
- R package to organise and standardise your genomic variant calls obtained with different callers.☆11Jul 15, 2019Updated 6 years ago
- Inferring selection in cancer sequencing data using ABC and population based simulations☆11Jan 31, 2021Updated 5 years ago
- Slides for my RLadies NYC Presentation☆11Feb 27, 2020Updated 5 years ago
- Somatic copy variant caller (CNV) for next generation sequencing☆75Sep 12, 2024Updated last year
- ☆12Nov 21, 2023Updated 2 years ago
- code for data processing and visualisation associated with the stromal subclasses manuscript☆13Oct 30, 2020Updated 5 years ago
- Implementation of FACETS for Terra☆12Jan 20, 2023Updated 3 years ago
- SelectiOn in PRotein ANnotated regiOns. Adapted dN/dS based method to detect selection in specific protein regions☆11May 2, 2024Updated last year
- SCCNV: a software tool for identifying copy number variation from single-cell whole-genome sequencing☆13Jul 21, 2020Updated 5 years ago
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆44Aug 24, 2022Updated 3 years ago
- Code accompanying The Evolutionary history of 2,658 cancers☆47Apr 16, 2021Updated 4 years ago
- Code used to generate the results in "Somatic chronology of treatment-resistant prostate cancer via deep whole-genome ctDNA sequencing"☆16Mar 11, 2024Updated last year
- Prostate Cancer Alteration Signature Analysis https://xsliulab.github.io/PC_CNA_signature/☆13May 17, 2021Updated 4 years ago
- R package to do enrichment analysis for neoantigens☆13Feb 21, 2022Updated 3 years ago
- mutSignatures R package - updated (dev) version - 2.1.4☆14Jan 18, 2023Updated 3 years ago
- Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R☆12Dec 6, 2021Updated 4 years ago
- A set of Pyro models and functions to infer CNA from scRNA-seq data☆11Aug 14, 2023Updated 2 years ago