This repository holds the companion project to Goby3, used to train and evaluate deep learning models to call variations. This repository contains the Matcha framework to help train and evaluate deep learning models trained with semi-simulation. See docs below for details.
☆52Jun 1, 2018Updated 8 years ago
Alternatives and similar repositories for variationanalysis
Users that are interested in variationanalysis are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆11Jul 13, 2018Updated 8 years ago
- filtering trio-based genetic variants in VCFs for clinical review☆22Aug 18, 2020Updated 6 years ago
- Gene lists related to cancer immunotherapy☆14Sep 11, 2024Updated last year
- iCAGES (integrated CAncer GEnome Score) is an effective tool for prioritizing cancer driver genes for a patient☆14Aug 18, 2022Updated 4 years ago
- Copy number estimation of highly duplicated sequences☆10Aug 15, 2017Updated 9 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.
- Extensible quality control dashboard built around FASTQ assessment.☆15May 17, 2019Updated 7 years ago
- A comprehensive pipeline to analyze and visualize structural variants☆20Jan 28, 2020Updated 6 years ago
- Simple matching of HTS samples based on HLA typing☆14Jan 4, 2017Updated 9 years ago
- ☆13May 2, 2018Updated 8 years ago
- Call regions of homozygosity and make tentative UPD calls☆12Jun 27, 2025Updated last year
- vgraph is a command line application and Python library to compare genetic variants using variant graphs. ``vgraph`` utilizes a graph re…☆43Sep 16, 2021Updated 4 years ago
- NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection☆175Dec 23, 2021Updated 4 years ago
- ABRA2☆97Dec 2, 2022Updated 3 years ago
- A Framework to call Structural Variants from NGS based datasets☆22Jan 22, 2018Updated 8 years ago
- 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.
- ☆13Jun 21, 2017Updated 9 years ago
- Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity☆40Jul 19, 2017Updated 9 years ago
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- Samwell: a python package for using genomic files... well☆20Jun 28, 2022Updated 4 years ago
- Benchmarking toolkit for variant calling☆48Oct 13, 2020Updated 5 years ago
- Calculates the Variant Allele Fraction of variants in VCF files☆19Nov 28, 2024Updated last year
- an R package for ancestry analysis☆37Jan 9, 2019Updated 7 years ago
- Repository for RecallME-v.0.1 a variant calling pipelines benchmarker and optimizer☆13Dec 18, 2023Updated 2 years ago
- paplot creates various dynamic and interactive reports for cancer genome analysis.☆26Feb 1, 2023Updated 3 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.
- CNV calling algorithm for detection of homozygous and hemizygous deletions from whole exome sequencing data☆12Nov 9, 2025Updated 9 months ago
- RUFUS k-mer based genomic variant detection☆55Jan 5, 2026Updated 7 months 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
- Analysis of Cancer Genomes; 2017 edition☆16Jan 21, 2018Updated 8 years ago
- Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…☆54Jun 5, 2017Updated 9 years ago
- pathoscore evaluates variant pathogenicity tools and scores.☆22Mar 25, 2022Updated 4 years ago
- Efficient C functions to compute the summary statistics (flagstats) for sequencing read sets.☆15Aug 1, 2026Updated last month
- Assembly Based ReAligner☆75May 24, 2018Updated 8 years ago
- robust matching of small variant datasets using flexible scoring schemes☆12Mar 26, 2020Updated 6 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- ☆23Sep 4, 2018Updated 7 years ago
- Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer☆21Dec 8, 2020Updated 5 years ago
- Data exploration with multiple machine learning algorithms☆14Nov 28, 2021Updated 4 years ago
- Structural Variation breakpoint discovery via adaptive learning☆17Jul 6, 2023Updated 3 years ago
- ☆42Jul 17, 2018Updated 8 years ago
- Recommended Graphtyper pipelines☆15Feb 22, 2021Updated 5 years ago
- Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model☆27Dec 26, 2023Updated 2 years ago