Jeltje / varscan2
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
- Documenting usage and experience with bioinformatic tools☆41Updated 9 years ago
- Tools for processing and analyzing structural variants.☆33Updated 9 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…☆31Updated 3 years ago
- R package for inferring copy number from read depth☆32Updated 2 years ago
- Detection of Circular RNA and Fusions from RNA-Seq☆32Updated 6 years ago
- Somatic variant identification from unpaired samples☆15Updated 8 years ago
- QDNAseq package for Bioconductor☆50Updated 9 months ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods☆46Updated 2 years ago
- Fork of the Polysolver project☆31Updated 5 years ago
- Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis☆21Updated 2 years ago
- CN-Learn☆29Updated 5 years ago
- ☆46Updated 5 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
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆44Updated 2 years ago
- A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.☆35Updated 3 years ago
- Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data☆27Updated last year
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆71Updated 11 months ago
- Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer☆47Updated this week
- SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …☆45Updated last month
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Updated 6 years ago
- RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.☆39Updated 3 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 4 years ago
- ☆13Updated 7 years ago
- SPP - R package for analysis of ChIP-seq and other functional sequencing data☆42Updated 3 years ago
- ☆38Updated 5 years ago
- ChIP-seq DC and QC Pipeline☆34Updated 4 years ago
- identifying mutational significance in cancer genomes☆61Updated 2 years ago
- Burden testing against public controls☆50Updated last year