AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more…
☆162Jun 18, 2024Updated 2 years ago
Alternatives and similar repositories for AmpliconArchitect
Users that are interested in AmpliconArchitect are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A quickstart tool for AmpliconArchitect. Enables all steps (alignment, CNV calling, seed interval detection) prior to running AmpliconArc…☆85Updated this week
- Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.☆30Oct 10, 2025Updated 9 months ago
- Classify output of AmpliconArchitect to detect types of focal amplifications present☆23Jul 22, 2026Updated last week
- Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data☆19Nov 13, 2023Updated 2 years ago
- Micro DNA identification☆24Aug 5, 2021Updated 4 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Code and data from Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020)☆15Nov 5, 2020Updated 5 years ago
- Tool used to quantify extrachromosomal DNA (ecDNA) in metaphase images stained with DAPI and FISH probes.☆19Updated this week
- A method for circular DNA detection based on probabilistic mapping of ultrashort reads☆68Jul 17, 2024Updated 2 years ago
- ☆80Jul 12, 2023Updated 3 years ago
- Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.☆12Jul 22, 2026Updated last week
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆73May 23, 2024Updated 2 years ago
- CoRAL: Reconstruction of focal amplifications with long reads☆31Updated this week
- Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from…☆35Updated this week
- A framework to infer mutational signatures in cancer over time☆58Jul 9, 2019Updated 7 years 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.
- ☆86Apr 17, 2025Updated last year
- R package containing useful functions for mutational signature analysis☆87Updated this week
- Various algorithms for analysing genomics data☆288Updated this week
- Structural variation and indel detection by local assembly☆256Jul 15, 2026Updated 2 weeks ago
- R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework☆42Updated this week
- Integrative analysis of complex structural variants☆22Sep 7, 2020Updated 5 years ago
- RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes☆19Apr 2, 2020Updated 6 years ago
- mutSignatures R package - updated (dev) version - 2.1.4☆14Jan 18, 2023Updated 3 years ago
- SV clustering☆31Jul 5, 2021Updated 5 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data☆178Aug 22, 2024Updated last year
- Copy number variant detection from targeted DNA sequencing☆616Updated this week
- DriverPower☆26Jan 18, 2025Updated last year
- isoCirc☆10Nov 27, 2023Updated 2 years ago
- HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jo…☆72Jul 8, 2026Updated 3 weeks ago
- iFISH Probe Design: a Python3 package to build iFISH probes.☆12Mar 11, 2022Updated 4 years ago
- GRIDSS: the Genomic Rearrangement IDentification Software Suite☆286May 21, 2025Updated last year
- ☆28Jun 14, 2026Updated last month
- Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.☆163Feb 12, 2026Updated 5 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- GCAP (Gene-level Circular Amplicon Prediction) firstly implements extrachromosomal DNA detection from whole-exome-sequencing (WES) data a…☆21Jul 1, 2026Updated 3 weeks ago
- Fast method for inferring cancer clonal population structure from SNV data.☆75Jan 20, 2026Updated 6 months ago
- dN/dS methods to quantify selection in cancer and somatic evolution☆237May 15, 2025Updated last year
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆101Updated this week
- ☆11Apr 25, 2024Updated 2 years ago
- Inferring CNV from Single-Cell RNA-Seq☆678Nov 14, 2025Updated 8 months ago
- R package for extracting and visualizing mutational patterns in base substitution catalogues☆107Nov 22, 2022Updated 3 years ago