amcpherson / citupLinks
Clonality inference in multiple tumor samples using phylogeny
☆13Updated 7 years ago
Alternatives and similar repositories for citup
Users that are interested in citup are comparing it to the libraries listed below
Sorting:
- ☆13Updated 7 years ago
- ☆19Updated 7 years ago
- All-FIT - Allele-Frequency-based Imputation of Tumor Purity☆17Updated 5 years ago
- Main repository for Drews et al. (Nature, 2022)☆41Updated last year
- Clonality Inference in Multiple Tumor Samples using Phylogeny☆14Updated 10 years ago
- Spatial Computational Inference of MEtastatic Timing (SCIMET)☆14Updated 6 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆31Updated last year
- Fork of the Polysolver project☆31Updated 5 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆29Updated 2 months ago
- This is a read-only mirror of the CRAN R package repository. sequenza — Copy Number Estimation from Tumor Genome Sequencing Data. Homep…☆19Updated 6 years ago
- Comprehensive genome-wide visualization of absolute copy number and copy neutral variations☆29Updated 6 years ago
- Fork of https://bitbucket.org/mcgranahanlab/lohhla☆17Updated 5 years ago
- High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants☆22Updated 5 years ago
- An R package for predicting HR deficiency from mutation contexts☆28Updated 3 months ago
- MutSig2CV from Lawrence et al. 2014☆31Updated 4 years ago
- Benchmarking of CNV calling tools☆18Updated 6 years ago
- Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data☆34Updated 6 months ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆71Updated last year
- Microsatellite instability (MSI) detection for cfDNA samples.☆19Updated 4 years ago
- Define regions in the genome☆30Updated 3 years ago
- This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …☆34Updated 10 months ago
- ☆11Updated 2 years ago
- SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …☆44Updated 2 months ago
- A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to …☆23Updated 3 years ago
- An R package to time somatic mutations☆61Updated 4 years ago
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Updated 2 years ago
- CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-frien…☆20Updated 5 years ago
- Utility functions for FACETS☆35Updated last year
- ☆17Updated 6 years ago
- Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis☆20Updated 2 years ago