Jeltje / varscan2Links
Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
☆29Updated 7 years ago
Alternatives and similar repositories for varscan2
Users that are interested in varscan2 are comparing it to the libraries listed below
Sorting:
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 6 years ago
- QDNAseq package for Bioconductor☆50Updated last year
- R package for inferring copy number from read depth☆32Updated 2 years ago
- identifying mutational significance in cancer genomes☆61Updated 2 years ago
- ⛏ HLA predictions from NGS shotgun data☆54Updated 2 months ago
- Documenting usage and experience with bioinformatic tools☆40Updated 9 years ago
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆47Updated 7 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 4 years ago
- ☆21Updated 2 weeks ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆31Updated 2 years ago
- Tumor Mutational Burden☆62Updated last week
- SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …☆46Updated 4 months ago
- Gene Fusion Visualiser☆51Updated 2 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
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆51Updated 3 years ago
- A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.☆35Updated 3 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆71Updated last year
- Fork of the Polysolver project☆31Updated 5 years ago
- Full-spectrum copy number variation detection by high-throughput DNA sequencing☆37Updated 3 years ago
- Snakemake-based workflow for detecting structural variants in genomic data☆80Updated 5 months ago
- Tools for analyzing DNA methylation data☆43Updated last week
- Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods☆46Updated 2 years ago
- Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests☆49Updated last year
- ☆13Updated 7 years ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆54Updated 4 years ago
- Detection of viruses from RNA-Seq on human samples☆45Updated 2 years ago
- Tools for processing and analyzing structural variants.☆33Updated 9 years ago
- RNA-seq workflow: differential transcript usage☆22Updated last year
- Somatic copy variant caller (CNV) for next generation sequencing☆73Updated 10 months ago
- R package designed to simplify structural variant analysis