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…
☆165Jun 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…☆87Sep 22, 2026Updated 3 weeks ago
- Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.☆30Oct 10, 2025Updated last year
- Classify output of AmpliconArchitect to detect types of focal amplifications present☆23Jul 22, 2026Updated 2 months ago
- Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data☆19Nov 13, 2023Updated 2 years ago
- Micro DNA identification☆24Aug 5, 2021Updated 5 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- 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.☆19Jul 28, 2026Updated 2 months ago
- A method for circular DNA detection based on probabilistic mapping of ultrashort reads☆69Jul 17, 2024Updated 2 years ago
- ☆81Jul 12, 2023Updated 3 years ago
- Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.☆13Sep 22, 2026Updated 3 weeks ago
- 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☆31Oct 8, 2026Updated last week
- Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from…☆35Oct 7, 2026Updated last week
- A framework to infer mutational signatures in cancer over time☆58Jul 9, 2019Updated 7 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.
- Various algorithms for analysing genomics data☆292Updated this week
- ☆86Apr 17, 2025Updated last year
- Structural variation and indel detection by local assembly☆259Aug 19, 2026Updated last month
- R package containing useful functions for mutational signature analysis☆90Updated this week
- Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data☆178Aug 22, 2024Updated 2 years ago
- R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework☆42Oct 5, 2026Updated last week
- Integrative analysis of complex structural variants☆22Sep 7, 2020Updated 6 years ago
- RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes☆19Apr 2, 2020Updated 6 years ago
- GRIDSS: the Genomic Rearrangement IDentification Software Suite☆286May 21, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- mutSignatures R package - updated (dev) version - 2.1.4☆14Jan 18, 2023Updated 3 years ago
- SV clustering☆32Jul 5, 2021Updated 5 years ago
- DriverPower☆26Jan 18, 2025Updated last year
- Copy number variant detection from targeted DNA sequencing☆616Updated this week
- 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…☆72Sep 29, 2026Updated 2 weeks ago
- iFISH Probe Design: a Python3 package to build iFISH probes.☆12Mar 11, 2022Updated 4 years ago
- Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.☆166Feb 12, 2026Updated 8 months ago
- ☆28Sep 11, 2026Updated last month
- 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.
- ASCAT R package☆205Feb 12, 2026Updated 8 months ago
- GCAP (Gene-level Circular Amplicon Prediction) firstly implements extrachromosomal DNA detection from whole-exome-sequencing (WES) data a…☆21Jul 1, 2026Updated 3 months ago
- Fast method for inferring cancer clonal population structure from SNV data.☆77Jan 20, 2026Updated 8 months ago
- Microsatellite Instability (MSI) detection using high-throughput sequencing data.☆118Apr 2, 2025Updated last year
- Fast and accurate gene fusion detection from RNA-Seq data☆281Sep 21, 2025Updated last year
- ☆12Apr 25, 2024Updated 2 years ago
- dN/dS methods to quantify selection in cancer and somatic evolution☆241Aug 25, 2026Updated last month