Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
☆44Aug 24, 2022Updated 3 years ago
Alternatives and similar repositories for alleleCount
Users that are interested in alleleCount are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Battenberg R package for subclonal copynumber estimation☆99May 11, 2026Updated 2 months ago
- ASCAT R package☆203Feb 12, 2026Updated 5 months ago
- Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation☆26Jul 17, 2026Updated last week
- Non-parametric structural variant genotyper☆15Nov 18, 2021Updated 4 years ago
- ☆19Apr 16, 2026Updated 3 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- 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 weeks ago
- cDriver R package for finding candidate driver genes in cancers☆18Jan 18, 2018Updated 8 years ago
- knowledge-based genotyping of cancer hotspots from the tumor BAM files☆22Dec 14, 2021Updated 4 years ago
- MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.☆59Jul 2, 2026Updated 3 weeks ago
- ☆11Apr 25, 2024Updated 2 years ago
- R pkg for Hierarchical Dirichlet Process☆86Jul 18, 2023Updated 3 years ago
- Python function for TMB snake plots☆16Feb 12, 2026Updated 5 months ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆71Nov 20, 2020Updated 5 years ago
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 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.
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆149Sep 9, 2020Updated 5 years ago
- Somatic copy variant caller (CNV) for next generation sequencing☆78Sep 12, 2024Updated last year
- ☆12Apr 26, 2020Updated 6 years ago
- A set of tools to annotate VCF files with expression and readcount data☆31Updated this week
- SV clustering☆31Jul 5, 2021Updated 5 years ago
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆44Aug 21, 2025Updated 11 months ago
- The "copynumber" R package with support for hg38☆21Apr 10, 2023Updated 3 years ago
- dN/dS methods to quantify selection in cancer and somatic evolution☆237May 15, 2025Updated last year
- Fast method for inferring cancer clonal population structure from SNV data.☆75Jan 20, 2026Updated 6 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A framework to infer mutational signatures in cancer over time☆58Jul 9, 2019Updated 7 years ago
- DriverPower☆26Jan 18, 2025Updated last year
- SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations o…☆123Jul 21, 2026Updated last week
- Allele-Specific Quantification of Structural Variations in Cancer Genomes☆19Mar 5, 2019Updated 7 years ago
- Comprehensive genome-wide visualization of absolute copy number and copy neutral variations☆29Apr 10, 2019Updated 7 years ago
- ☆18Jan 30, 2023Updated 3 years ago
- Python program designed to reconstruct immunoglobulin gene rearrangements and oncogenic translocations from WGS, WES and capture NGS in l…☆21Jul 6, 2023Updated 3 years ago
- Utility functions for FACETS☆40Oct 24, 2025Updated 9 months ago
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Jul 7, 2018Updated 8 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer sampl…☆85Apr 24, 2025Updated last year
- ☆13Jan 23, 2020Updated 6 years ago
- Structural Variant Prediction Viewer☆35Jul 19, 2017Updated 9 years ago
- R package designed to simplify structural variant analysis☆74Dec 22, 2021Updated 4 years ago
- deconstructSigs☆144Apr 24, 2023Updated 3 years ago
- Toolkit for extracting SVs from long sequences and benchmarking variant callers☆13Jan 10, 2017Updated 9 years ago
- v2.x of the microassembly based somatic variant caller☆29Jun 30, 2026Updated 3 weeks ago