Alternatives and similar repositories for varscan2:

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

• jlab-code / MethylStar
  A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
  ☆35Updated 3 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago
• LosicLab / starchip
  Detection of Circular RNA and Fusions from RNA-Seq
  ☆32Updated 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…
  ☆31Updated 3 years ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 2 years ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆42Updated 7 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• stephenfloor / extract-transcript-regions
  For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…
  ☆35Updated last year
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆38Updated 3 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• pughlab / ConsensusCruncher
  ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…
  ☆21Updated 2 years ago
• ikalatskaya / ISOWN
  ☆46Updated 5 years ago
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆52Updated last month
• nspies / svviz2
  for visual evaluation of read support for structural variation
  ☆52Updated 9 months ago
• bjtrost / TCAG-WGS-CNV-workflow
  Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods
  ☆46Updated 2 years ago
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆38Updated last month
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆33Updated 9 years ago
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 4 years ago
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 8 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆49Updated 7 months ago
• DecodeGenetics / svimmer
  Structural variant merging tool
  ☆49Updated 7 months ago
• imbforge / NGSpipe2go
  a set of NGS pipelines
  ☆24Updated 2 weeks ago
• kylessmith / SomVarIUS
  Somatic variant identification from unpaired samples
  ☆15Updated 8 years ago
• ndbrown6 / MSK-GRAIL-TECHVAL
  High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
  ☆22Updated 4 years ago
• jason-weirather / hla-polysolver
  Fork of the Polysolver project
  ☆31Updated 5 years ago
• molgenis / capice
  ☆23Updated 3 months ago
• jsh58 / DMRfinder
  Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data
  ☆27Updated last year
• TomSkelly / MatchAnnot
  Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.
  ☆23Updated 9 years ago
• girirajanlab / CN_Learn
  CN-Learn
  ☆29Updated 5 years ago