kharchenkolab / hahmmrView external linksLinks
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
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
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 5 years ago
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆202Feb 4, 2026Updated last week
- Polyidus provides a framework to catch chimeric DNA sequences with a tale of python☆10Jul 14, 2023Updated 2 years ago
- Scripts and files used in the generation of the COLO829 somatic SV truthset.☆13Apr 9, 2022Updated 3 years ago
- ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) is a novel framework for the inference of a set of statistically significant temporal pa…☆12Apr 18, 2025Updated 9 months ago
- A guide to using the Python scRNA-seq analysis package Scanpy from R☆15Apr 27, 2020Updated 5 years ago
- ☆16Sep 1, 2023Updated 2 years ago
- Workflow to reproduce results and figures for the second BeatAML manuscript☆14Jun 28, 2022Updated 3 years ago
- Computational identification of targets for CAR-T cell therapy in AML☆21Dec 25, 2022Updated 3 years ago
- Vaeda method for computational doublet annotation☆18Feb 1, 2026Updated 2 weeks ago
- Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…☆42Apr 18, 2024Updated last year
- Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.☆38Jan 22, 2026Updated 3 weeks ago
- Pairwise Hierarchical Model☆20Mar 11, 2022Updated 3 years ago
- An R package to plot maps of clone distributions in somatic evolution☆19Jan 8, 2024Updated 2 years ago
- A web application from the Raphael Lab for mutation annotation and genome interpretation.☆20Feb 16, 2018Updated 8 years ago
- ☆17Jul 13, 2024Updated last year
- Single-cell Case Control Analysis☆52Jan 29, 2026Updated 2 weeks ago
- A Rust library for storing generic genomic data by sorted chromosome name☆17Sep 26, 2024Updated last year
- Artisanal 🤣 bioinformatics tools and pipelines in Scala☆20Jan 28, 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 5 months ago
- Human Endometrial Cell Atlas (HECA). An integrated single-cell reference atlas of the human endometrium.☆30Jun 19, 2024Updated last year
- R wrapper for utilizing the SigProfilerMatrixGenerator framework☆20Jan 29, 2026Updated 2 weeks ago
- RNA velocity validation☆22Mar 16, 2022Updated 3 years ago
- Efficient genotyping bi-allelic SNPs on single cells☆157Oct 30, 2025Updated 3 months ago
- ☆22Mar 6, 2023Updated 2 years ago
- General Purpose Optimization in R using C++: provides a unified C++ wrapper to call functions of the algorithms underlying the optim() s…☆21Oct 2, 2025Updated 4 months ago
- Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition☆63Apr 14, 2024Updated last year
- HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jo…☆70Feb 26, 2025Updated 11 months ago
- A framework to infer mutational signatures in cancer over time☆56Jul 9, 2019Updated 6 years ago
- scover☆24Nov 3, 2023Updated 2 years ago
- An information-theoretic pipeline for methylation analysis of WGBS data☆24Apr 9, 2019Updated 6 years ago
- Clone identification from single-cell data☆61Nov 10, 2022Updated 3 years ago
- Analyzing cellular niches in spatial transcriptomics data☆34Nov 18, 2024Updated last year
- Somatic point mutation caller☆33Jan 7, 2026Updated last month
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆151Updated this week
- Exploring dimension-reduced embeddings☆111Jul 6, 2022Updated 3 years ago
- Cell age determination by scATAC-seq and bulk-ATAC-seq☆33Jan 30, 2026Updated 2 weeks ago
- R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after cor…☆32Oct 29, 2025Updated 3 months ago