Alternatives and similar repositories for PennCNV:

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

• 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…
  ☆52Updated 4 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆70Updated 4 years ago
• ding-lab / CharGer
  Characterization of Germline variants
  ☆98Updated 2 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆82Updated 7 years ago
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated 11 months ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆96Updated 9 months ago
• slowkow / snakefiles
  Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
  ☆92Updated 7 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 3 months ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆72Updated 3 years ago
• Illumina / Polaris
  Data and information about the Polaris study
  ☆53Updated 5 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆96Updated 3 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆128Updated 8 months ago
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆70Updated 7 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆96Updated 2 years ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆132Updated last month
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆52Updated 5 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆45Updated 6 years ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆67Updated 5 months ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆60Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 3 months ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• Genotek / ClassifyCNV
  ClassifyCNV: a tool for clinical annotation of copy-number variants
  ☆60Updated last year
• RahmanTeam / DECoN
  ☆52Updated 2 years ago
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆77Updated 4 years ago
• freeseek / score
  Tools to work with GWAS-VCF summary statistics files
  ☆113Updated 4 months ago
• eQTL-Catalogue / qtlmap
  Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue
  ☆46Updated this week
• xihaoli / STAARpipeline
  An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline
  ☆62Updated last week
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆96Updated 5 months ago