Alternatives and similar repositories for varscan2

Users that are interested in varscan2 are comparing it to the libraries listed below

• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 3 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆54Updated last year
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆55Updated 7 months ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆62Updated 3 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• dnaase / Bis-tools
  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…
  ☆32Updated 4 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆63Updated 5 months ago
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆34Updated 10 years ago
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆44Updated last week
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆100Updated 4 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆53Updated 3 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆41Updated 3 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• zd1 / telseq
  A software for calculating telomere length
  ☆73Updated 7 years ago
• jlab-code / MethylStar
  A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
  ☆37Updated 4 years ago
• Oshlack / Clinker
  Gene Fusion Visualiser
  ☆51Updated 3 years ago
• WGLab / VirTect
  Detection of viruses from RNA-Seq on human samples
  ☆46Updated 2 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆40Updated 4 years ago
• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆55Updated 5 years ago
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• ikalatskaya / ISOWN
  ☆46Updated 6 years ago
• a2iEditing / RNAEditingIndexer
  A tool for the calculation of RNA-editing index for RNA seq data
  ☆45Updated last week
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆75Updated last year
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆82Updated 11 months ago
• jason-weirather / hla-polysolver
  Fork of the Polysolver project
  ☆33Updated 6 years ago
• mskilab-org / JaBbA
  MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
  ☆59Updated 9 months ago
• thelovelab / rnaseqDTU
  RNA-seq workflow: differential transcript usage
  ☆23Updated 2 years ago
• ChrisMaherLab / ClonEvol
  ☆13Updated 8 years ago
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year