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 4 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☆101May 11, 2026Updated 3 months ago
- ASCAT R package☆204Feb 12, 2026Updated 6 months ago
- Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation☆27Aug 31, 2026Updated last week
- Non-parametric structural variant genotyper☆15Nov 18, 2021Updated 4 years ago
- ☆19Apr 16, 2026Updated 4 months 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.
- 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 2 months 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 2 months 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 6 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
- 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.
- 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☆79Sep 12, 2024Updated last year
- ☆12Apr 26, 2020Updated 6 years ago
- A set of tools to annotate VCF files with expression and readcount data☆31Aug 17, 2026Updated 2 weeks ago
- SV clustering☆32Jul 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 last year
- 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☆240Aug 25, 2026Updated last week
- Fast method for inferring cancer clonal population structure from SNV data.☆77Jan 20, 2026Updated 7 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- BigWig manpulation tools using libBigWig and htslib☆30Aug 8, 2024Updated 2 years ago
- 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…☆123Aug 25, 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☆30Apr 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…☆22Jul 6, 2023Updated 3 years ago
- Utility functions for FACETS☆40Oct 24, 2025Updated 10 months ago
- 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.
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Jul 7, 2018Updated 8 years ago
- SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer sampl…☆86Apr 24, 2025Updated last year
- ☆13Jan 23, 2020Updated 6 years ago
- Structural Variant Prediction Viewer☆36Jul 19, 2017Updated 9 years ago
- R package designed to simplify structural variant analysis☆74Dec 22, 2021Updated 4 years ago
- deconstructSigs☆145Apr 24, 2023Updated 3 years ago
- Toolkit for extracting SVs from long sequences and benchmarking variant callers☆12Jan 10, 2017Updated 9 years ago