raphael-group / hatchetLinks
HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.
☆70Updated 9 months ago
Alternatives and similar repositories for hatchet
Users that are interested in hatchet are comparing it to the libraries listed below
Sorting:
- Reconstruction of focal amplifications with long reads☆22Updated 3 weeks ago
- SingleCell Nanopore sequencing data analysis☆63Updated 6 months ago
- fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector☆22Updated last month
- GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.☆44Updated 8 years ago
- A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…☆32Updated 4 years ago
- Micro DNA identification☆24Updated 4 years ago
- ☆23Updated 11 months ago
- SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3☆38Updated 5 years ago
- SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …☆51Updated last month
- Find and characterise transposable element insertions☆20Updated 2 years ago
- Runs a combination of tools to generate structural variant calls on whole-genome sequencing data☆48Updated 5 years ago
- Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.☆41Updated 4 years ago
- ENCODE whole-genome bisulfite sequencing (WGBS) pipeline☆32Updated 3 years ago
- ENCODE long read RNA-seq pipeline☆51Updated 2 years ago
- ⛏ HLA predictions from NGS shotgun data☆55Updated 5 months ago
- An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.☆54Updated last year
- ClairS-TO - a deep-learning method for tumor-only somatic variant calling☆75Updated 2 weeks ago
- ☆38Updated 2 years ago
- LongcallR is a SNP caller for single molecule long-read RNA-seq data☆69Updated 2 months ago
- Software to compute reproducibility and quality scores for Hi-C data☆49Updated 6 years ago
- ☆49Updated 2 years ago
- Tools for processing and analyzing structural variants.☆33Updated 10 years ago
- BSMN common data processing pipeline☆11Updated 5 months ago
- Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu☆15Updated last month
- Long-read Isoform Quantification and Analysis☆38Updated 8 months ago
- Snakemake-based workflow for detecting structural variants in genomic data☆80Updated 9 months ago
- MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.☆59Updated 8 months ago
- ☆44Updated last year
- A comprehensive toolkit for mutational signature analysis☆42Updated last year
- IDR☆31Updated 2 years ago