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☆95May 11, 2026Updated 2 weeks ago
- ASCAT R package☆200Feb 12, 2026Updated 3 months ago
- Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation☆26Jan 28, 2026Updated 4 months ago
- Non-parametric structural variant genotyper☆15Nov 18, 2021Updated 4 years ago
- cDriver R package for finding candidate driver genes in cancers☆18Jan 18, 2018Updated 8 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.
- This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…☆18Mar 24, 2026Updated 2 months 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.☆59Mar 23, 2025Updated last year
- ☆11Apr 25, 2024Updated 2 years ago
- R pkg for Hierarchical Dirichlet Process☆85Jul 18, 2023Updated 2 years ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆72Nov 20, 2020Updated 5 years ago
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- 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
- 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.
- ☆12Apr 26, 2020Updated 6 years ago
- Python function for TMB snake plots☆16Feb 12, 2026Updated 3 months ago
- A set of tools to annotate VCF files with expression and readcount data☆30Jan 30, 2026Updated 3 months ago
- The "copynumber" R package with support for hg38☆21Apr 10, 2023Updated 3 years ago
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆44Aug 21, 2025Updated 9 months ago
- SV clustering☆31Jul 5, 2021Updated 4 years ago
- A framework to infer mutational signatures in cancer over time☆58Jul 9, 2019Updated 6 years ago
- DriverPower☆26Jan 18, 2025Updated last year
- dN/dS methods to quantify selection in cancer and somatic evolution☆235May 15, 2025Updated last year
- 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.
- SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations o…☆121Updated this week
- Allele-Specific Quantification of Structural Variations in Cancer Genomes☆18Mar 5, 2019Updated 7 years ago
- Comprehensive genome-wide visualization of absolute copy number and copy neutral variations☆29Apr 10, 2019Updated 7 years ago
- BigWig manpulation tools using libBigWig and htslib