amcpherson / citupLinks
Clonality inference in multiple tumor samples using phylogeny
☆13Updated 8 years ago
Alternatives and similar repositories for citup
Users that are interested in citup are comparing it to the libraries listed below
Sorting:
- ☆13Updated 8 years ago
- Fork of the Polysolver project☆33Updated 5 years ago
- Main repository for Drews et al. (Nature, 2022)☆42Updated 2 years ago
- Spatial Computational Inference of MEtastatic Timing (SCIMET)☆14Updated 6 years ago
- Define regions in the genome☆33Updated 3 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆31Updated 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, …☆50Updated last week
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 6 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆71Updated last year
- Filters for false-positive mutation calls in NGS☆34Updated 6 years ago
- This is a read-only mirror of the CRAN R package repository. sequenza — Copy Number Estimation from Tumor Genome Sequencing Data. Homep…☆20Updated 6 years ago
- This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …☆34Updated last month
- ☆19Updated 7 years ago
- 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
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆52Updated 3 years ago
- ☆21Updated last week
- BISulfite-seq CUI Toolkit☆24Updated last month
- Burden testing against public controls☆50Updated last year
- Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data☆35Updated 10 months ago
- CLIP-seq Analysis of Multi-mapped reads☆31Updated 4 years ago
- ☆26Updated last year
- chia pet analysis software☆25Updated 6 years ago
- A comprehensive toolkit for mutational signature analysis☆41Updated last year
- Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.☆41Updated 4 years ago
- Benchmarking of CNV calling tools☆18Updated 6 years ago
- A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…☆32Updated 3 years ago
- ☆36Updated 6 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆30Updated 6 months ago
- An R package for predicting HR deficiency from mutation contexts☆29Updated 8 months ago
- An R package to time somatic mutations☆64Updated 4 years ago