Git repo for CONIPHER tree building
☆27Mar 20, 2025Updated last year
Alternatives and similar repositories for CONIPHER
Users that are interested in CONIPHER are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Spatial Computational Inference of MEtastatic Timing (SCIMET)☆14May 28, 2019Updated 7 years ago
- ☆11May 26, 2023Updated 3 years ago
- CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-frien…☆21Jan 17, 2020Updated 6 years ago
- R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after cor…☆32Oct 29, 2025Updated 10 months ago
- Framework for Metastatic And Clonal History INtegrative Analysis☆37Mar 5, 2021Updated 5 years 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.
- ☆13Nov 21, 2023Updated 2 years ago
- Application for inferring subclonal composition and evolution from whole-genome sequencing data.☆114Oct 12, 2022Updated 3 years ago
- Clonality inference in multiple tumor samples using phylogeny☆14Sep 12, 2017Updated 8 years ago
- ☆14Apr 4, 2023Updated 3 years ago
- Total copy number inference from single-cell RNA and ATAC sequing with cell clustering☆12Oct 31, 2024Updated last year
- HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jo…☆72Jul 31, 2026Updated last month
- ☆11Apr 25, 2024Updated 2 years ago
- Visualization tool for temporal clonal evolution.☆18Mar 13, 2020Updated 6 years ago
- A robust PCA method of tumor clone and evolution inference from single-cell sequencing data.☆12May 28, 2020Updated 6 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Data Structures for Bioinformatics - LM Bioinformatics - University of Rome Tor Vergata☆12Feb 27, 2026Updated 6 months ago
- QBRC Neoantigen calling pipeline with CSiN calculation embedded☆26Feb 8, 2022Updated 4 years ago
- CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk …☆15Nov 28, 2023Updated 2 years ago
- Code accompanying "The evolutionary history of 2,658 cancers", Nature 578, 122–128 (2020)☆17Jan 15, 2020Updated 6 years ago
- ASCAT R package☆204Feb 12, 2026Updated 6 months ago
- Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data☆14Dec 24, 2023Updated 2 years ago
- cDriver R package for finding candidate driver genes in cancers☆18Jan 18, 2018Updated 8 years ago
- Fast, self-contained VCF to MAF converter with embedded annotation (Rust rewrite of vcf2maf)☆22Jun 23, 2026Updated 2 months ago
- DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell frac…☆22May 21, 2024Updated 2 years ago
- 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.
- Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes☆44Apr 16, 2021Updated 5 years ago
- Pipeline used to test for an enrichment of sweeps in a set of genes while controlling for confounding factors and with the option to run …☆18Apr 28, 2021Updated 5 years ago
- <Bioinformatics> scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution☆27Aug 27, 2025Updated last year
- LACE 2.0 is a new release of the LACE R Bioconductor package, which provides an interactive user interface to perform clonal evolution an…☆16Apr 7, 2026Updated 4 months ago
- ☆39Aug 7, 2026Updated 3 weeks ago
- Snakemake workflow for neoantigen prediction☆15Sep 7, 2023Updated 2 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆32Jul 27, 2023Updated 3 years ago
- Codes and Data for FFPEsig manuscript☆16Jan 17, 2024Updated 2 years ago
- Python program designed to reconstruct immunoglobulin gene rearrangements and oncogenic translocations from WGS, WES and capture NGS in l…☆22Jul 6, 2023Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- An R package to plot maps of clone distributions in somatic evolution☆20Aug 3, 2026Updated 3 weeks ago
- Genomic Identification of Significant Targets in Cancer (GISTIC), version 2☆53Apr 8, 2022Updated 4 years ago
- SNV calling from single cell sequencing☆119Nov 11, 2024Updated last year
- Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.☆71Aug 22, 2021Updated 5 years ago
- This R package contains codes that setup SEER and A-bomb survivor data use with R.☆14Jul 8, 2026Updated last month
- Command line client and Python libraries for CosmosID API☆13Oct 28, 2025Updated 10 months ago
- BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA☆16Apr 13, 2021Updated 5 years ago