Alternatives and similar repositories for pcgr

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

• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆146Updated 2 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆160Updated 2 years ago
• mskcc / facets
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆149Updated 2 years ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆222Updated last month
• VanLoo-lab / ascat
  ASCAT R package
  ☆183Updated 3 months ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆162Updated 10 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆269Updated last month
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆261Updated this week
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆254Updated 2 years ago
• gagneurlab / drop
  Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
  ☆149Updated 2 weeks ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆196Updated 2 weeks ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆269Updated last year
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆252Updated 4 months ago
• oncokb / oncokb-annotator
  Annotates variants in MAF with OncoKB annotation.
  ☆131Updated last week
• WGLab / InterVar
  A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
  ☆196Updated 2 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆213Updated 2 months ago
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆137Updated 4 years ago
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆219Updated last year
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆387Updated 6 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆243Updated 3 months ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆132Updated last year
• virajbdeshpande / AmpliconArchitect
  AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and …
  ☆147Updated last year
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated last week
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆202Updated 4 years ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆265Updated 2 years ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆275Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆199Updated last year