Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq
☆13Apr 2, 2024Updated last year
Alternatives and similar repositories for hahmmr
Users that are interested in hahmmr are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- This is the repository accompanying the pre-print titled, "Genome-wide analyses of 200,453 individuals yield new insights into the causes…☆13Jun 9, 2022Updated 3 years ago
- A guide to using the Python scRNA-seq analysis package Scanpy from R☆15Apr 27, 2020Updated 5 years ago
- An R package to plot maps of clone distributions in somatic evolution☆20Jan 8, 2024Updated 2 years ago
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆208Feb 4, 2026Updated last month
- Vaeda method for computational doublet annotation☆19Feb 1, 2026Updated last month
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) is a novel framework for the inference of a set of statistically significant temporal pa…☆12Apr 18, 2025Updated 11 months ago
- ☆17Jul 13, 2024Updated last year
- Polyidus provides a framework to catch chimeric DNA sequences with a tale of python☆10Jul 14, 2023Updated 2 years ago
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 6 years ago
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆42Aug 21, 2025Updated 7 months ago
- Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…☆42Apr 18, 2024Updated last year
- R wrapper for utilizing the SigProfilerMatrixGenerator framework☆20Jan 29, 2026Updated 2 months ago
- General Purpose Optimization in R using C++: provides a unified C++ wrapper to call functions of the algorithms underlying the optim() s…☆22Oct 2, 2025Updated 5 months ago
- Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data☆14Dec 24, 2023Updated 2 years ago
- Wordpress hosting with auto-scaling on Cloudways • AdFully Managed hosting built for WordPress-powered businesses that need reliable, auto-scalable hosting. Cloudways SafeUpdates now available.
- Computational identification of targets for CAR-T cell therapy in AML☆21Dec 25, 2022Updated 3 years ago
- Pairwise Hierarchical Model☆20Mar 11, 2022Updated 4 years ago
- Scripts and files used in the generation of the COLO829 somatic SV truthset.☆14Apr 9, 2022Updated 3 years ago
- A Rust library for storing generic genomic data by sorted chromosome name☆17Sep 26, 2024Updated last year
- Single-cell Case Control Analysis☆54Feb 26, 2026Updated last month
- Efficient genotyping bi-allelic SNPs on single cells☆158Oct 30, 2025Updated 5 months ago
- Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.☆38Jan 22, 2026Updated 2 months ago
- Cell age determination by scATAC-seq and bulk-ATAC-seq☆33Jan 30, 2026Updated 2 months ago
- Workflow to reproduce results and figures for the second BeatAML manuscript☆15Jun 28, 2022Updated 3 years ago
- Wordpress hosting with auto-scaling on Cloudways • AdFully Managed hosting built for WordPress-powered businesses that need reliable, auto-scalable hosting. Cloudways SafeUpdates now available.
- 一条命令就能安装精心打磨的工作流、命令、代理、MCP服务器和钩子☆31Oct 29, 2025Updated 5 months ago
- abi2fastq is a small utility to convert Sanger sequencing reads in .abi (applied biosystems) format to FASTQ☆11Sep 19, 2017Updated 8 years ago
- Materials accompanying the upstrap paper☆12Oct 19, 2020Updated 5 years ago
- Artisanal 🤣 bioinformatics tools and pipelines in Scala☆20Jan 28, 2020Updated 6 years ago
- ☆22Mar 6, 2023Updated 3 years ago
- ☆16Sep 1, 2023Updated 2 years ago
- Cloud-based molecular docking for everyone☆12Jul 1, 2024Updated last year
- SClineager: a Bayesian hierarchical model that performs lineage tracing of single cells based on genetic markers☆10Apr 30, 2024Updated last year
- A web application from the Raphael Lab for mutation annotation and genome interpretation.☆20Feb 16, 2018Updated 8 years ago
- 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.
- Human Endometrial Cell Atlas (HECA). An integrated single-cell reference atlas of the human endometrium.☆31Jun 19, 2024Updated last year
- ☆16May 8, 2023Updated 2 years ago
- Analyzing cellular niches in spatial transcriptomics data☆34Nov 18, 2024Updated last year
- HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jo…☆71Mar 19, 2026Updated last week
- Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition☆64Apr 14, 2024Updated last year
- Clone identification from single-cell data☆63Nov 10, 2022Updated 3 years ago
- Tree hidden Markov model for learning epigenetic states in multiple cell types☆28Jul 11, 2013Updated 12 years ago