a parallel R package for detecting copy-number alterations from short sequencing reads
☆24Jul 15, 2021Updated 5 years ago
Alternatives and similar repositories for copyCat
Users that are interested in copyCat are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Computes various SV statistics☆13Oct 12, 2023Updated 3 years ago
- West Coast Dream Team Whole Genome Bisulfite Sequencing☆17Nov 7, 2025Updated 11 months ago
- Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.☆72Aug 22, 2021Updated 5 years ago
- ☆10May 31, 2022Updated 4 years ago
- ☆44Nov 18, 2019Updated 6 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.
- Code for "Single cell transcriptomes from human kidneys reveal the cellular identity of renal tumours"☆27Jun 5, 2018Updated 8 years ago
- This repository contains HCA Benchmarking codes☆27Nov 11, 2019Updated 6 years ago
- This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…☆20Jul 6, 2026Updated 3 months ago
- knowledge-based genotyping of cancer hotspots from the tumor BAM files☆22Dec 14, 2021Updated 4 years ago
- Pipeline of tools to process raw fastq data and produce meaningful genomic data☆14Feb 20, 2020Updated 6 years ago
- An R package for inferring the subclonal architecture of tumors☆125Mar 15, 2026Updated 7 months ago
- Whole genome workflows☆13Nov 9, 2024Updated last year
- Create timecourse "fish plots" that show changes in the clonal architecture of tumors☆171Jan 28, 2026Updated 9 months ago
- Papillomavirus genome annotation tool☆10May 2, 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.
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Oct 26, 2018Updated 8 years ago
- Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data☆21Aug 19, 2020Updated 6 years ago
- Implementation of FACETS for Terra☆12Jan 20, 2023Updated 3 years ago
- ☆48Apr 18, 2020Updated 6 years ago
- MASCoTE (Multiple Allele-specific Simulation of Copy-number Tumor Evolution) is a simulation framework to generate sequencing reads with …☆13Dec 3, 2020Updated 5 years ago
- ☆12Feb 14, 2023Updated 3 years ago
- Code for creating cell-type-specific regulatory element annotation files☆21Jun 11, 2024Updated 2 years ago
- Clinical Variant Annotation Pipeline☆10Apr 21, 2020Updated 6 years ago
- Single Cell RNA Intron-Exon counting☆12May 7, 2020Updated 6 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.
- cancereffectsizeR: An R package for calculation of somatic mutation rates and quantification of selection in cancer☆20Oct 6, 2026Updated 3 weeks ago
- Fast fusion detection using kallisto☆80Jun 11, 2025Updated last year
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆151Sep 9, 2020Updated 6 years ago
- R package for inferring copy number from read depth☆33Sep 30, 2022Updated 4 years ago
- Single-cell analytic toolbox that offers modular workflows for multi-level cellular annotation and user-friendly analysis reports☆11Mar 31, 2026Updated 6 months ago
- A tool to examine duplicate read characteristics in a BAM file☆12Dec 8, 2017Updated 8 years ago
- Integrated workflow for SV calling from single-cell Strand-seq data☆26Oct 19, 2026Updated last week
- Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.☆29Feb 12, 2021Updated 5 years ago
- Repository for supplemental material of manuscripts☆19Jun 30, 2021Updated 5 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.
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆420May 25, 2026Updated 5 months ago
- R package to impute methylation within WGBS using machine learning☆13Mar 9, 2023Updated 3 years ago
- BISulfite-seq CUI Toolkit☆29Oct 5, 2026Updated 3 weeks ago
- Legacy, see cancerit/PCAP-core: NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project☆14Jun 12, 2024Updated 2 years ago
- ☆12Apr 26, 2020Updated 6 years ago
- Integrated copy number variation detection toolset☆26Feb 12, 2020Updated 6 years ago
- Personalized prioritization of driver genes in cancer☆10Mar 14, 2022Updated 4 years ago