Fork of https://bitbucket.org/mcgranahanlab/lohhla
☆18Feb 19, 2020Updated 6 years ago
Alternatives and similar repositories for LOHHLA
Users that are interested in LOHHLA are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Fork of the Polysolver project☆33Nov 21, 2019Updated 6 years ago
- BAMixChecker: A fast and efficient tool for sample matching checkup☆16Jun 12, 2022Updated 4 years ago
- iAnnotateSV is a Python library and command-line software toolkit to annotate and visualize structural variants detected from Next Genera…☆16Jun 11, 2026Updated 2 months ago
- CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-frien…☆21Jan 17, 2020Updated 6 years ago
- Workflow: Convert CONTROL-freec output to GISTIC2☆10Apr 20, 2021Updated 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.
- Detecting somatic mutations and predicting tumor-specific neo-antigens☆29Aug 10, 2021Updated 5 years ago
- All-FIT - Allele-Frequency-based Imputation of Tumor Purity☆18Oct 5, 2019Updated 6 years ago
- xHLA: Fast and accurate HLA typing from short read sequence data☆117Oct 13, 2023Updated 2 years ago
- Somatic point mutation caller☆17Jul 8, 2016Updated 10 years ago
- NeoDisc - A computational pipeline for the identification and prioritization of immunogenic tumor-specific HLA-I and -II antigens from ge…☆14Oct 8, 2024Updated last year
- ☆13Nov 21, 2023Updated 2 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆32Jul 27, 2023Updated 3 years ago
- Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.☆118Sep 2, 2024Updated 2 years ago
- Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R☆14Dec 6, 2021Updated 4 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.
- Clonality inference in multiple tumor samples using phylogeny☆14Sep 12, 2017Updated 8 years ago
- CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk …☆15Nov 28, 2023Updated 2 years ago
- Detecting TCR involved in immune responses from single RepSeq datasets☆28Jun 17, 2019Updated 7 years ago
- ☆28Jun 14, 2026Updated 2 months ago
- Singularity port of HLA typing based on an input exome BAM file and is currently infers infers alleles for the three major MHC class I (…☆15Jan 15, 2017Updated 9 years ago
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆149Sep 9, 2020Updated 5 years ago
- ☆17Dec 29, 2025Updated 8 months ago
- A Nextflow workflow for HLA typing using HLA-HD☆15Jul 3, 2024Updated 2 years ago
- Easy Copy Number !☆22Aug 27, 2025Updated last year
- 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.
- Model-based tumour subclonal deconvolution using population genetics☆36Dec 2, 2025Updated 9 months ago
- Clonality Inference in Multiple Tumor Samples using Phylogeny☆15May 8, 2015Updated 11 years ago
- NOTE: This package has been renamed to sparrow and will be submitted to Bioconductor 3.14. Please use that package instead. This is kept …☆23Nov 16, 2020Updated 5 years ago
- Snakemake workflow for neoantigen prediction☆15Sep 7, 2023Updated 3 years ago
- Simple matching of HTS samples based on HLA typing☆14Jan 4, 2017Updated 9 years ago
- Reference data: BED files, genes, transcripts, variations.☆90Nov 28, 2017Updated 8 years ago
- Short reads aligner for NIPT/CNV☆16Oct 10, 2018Updated 7 years ago
- Fast method for inferring cancer clonal population structure from SNV data.☆77Jan 20, 2026Updated 7 months ago
- HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jo…☆72Jul 31, 2026Updated last month
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- ABSOLUTE source code that works with allelic copy ratio on both hg19 and hg38☆18Nov 5, 2025Updated 10 months ago
- Python package to annotate and visualize gene fusions.☆66Apr 14, 2026Updated 4 months ago
- A Tidy Framework to Hack Gene Expression Signatures☆20Apr 20, 2025Updated last year
- Decrypting somatic mutation patterns to reveal the evolution of cancer☆57Mar 10, 2021Updated 5 years ago
- MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.☆52Sep 12, 2019Updated 6 years ago
- Pipeline for Somatic Variant Calling with WES and WGS data☆24May 7, 2024Updated 2 years ago
- Flexible and efficient tests for evidence of positive selection anywhere in the cancer genome.☆27Jul 30, 2022Updated 4 years ago