Alternatives and similar repositories for PennCNV

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

• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 7 months 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…
  ☆53Updated 4 years ago
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆115Updated 10 months ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆134Updated last month
• ding-lab / CharGer
  Characterization of Germline variants
  ☆98Updated 3 years ago
• odelaneau / shapeit5
  Segmented HAPlotype Estimation and Imputation Tool
  ☆80Updated 9 months ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• slowkow / snakefiles
  Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
  ☆93Updated 7 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 4 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆83Updated 7 years ago
• bmvdgeijn / WASP
  WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
  ☆105Updated 4 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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 5 years ago
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆132Updated 11 months ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆141Updated 2 years ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆71Updated 8 months ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• freeseek / mocha
  MOsaic CHromosomal Alterations (MoChA) caller
  ☆86Updated 3 months ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆69Updated 9 months ago
• francois-a / fastqtl
  Enhanced version of the FastQTL QTL mapper
  ☆65Updated 2 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆106Updated last year
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆56Updated 4 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆145Updated 2 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated 10 months ago
• sztup / scarHRD
  ☆115Updated last year
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆72Updated 3 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆87Updated 8 months ago