Alternatives and similar repositories for reference_data

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

• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆137Updated last year
• sztup / scarHRD
  ☆119Updated 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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…
  ☆78Updated 5 years ago
• ding-lab / msisensor
  microsatellite instability detection using tumor only or paired tumor-normal data
  ☆132Updated 5 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆100Updated 4 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆142Updated 3 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 4 months ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆113Updated last year
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 5 years ago
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆111Updated 2 months ago
• xjtu-omics / msisensor-pro
  Microsatellite Instability (MSI) detection using high-throughput sequencing data.
  ☆115Updated 10 months ago
• shendurelab / cfDNA
  Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA
  ☆78Updated 5 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆117Updated last year
• FoundationMedicineInc / SGZ
  ☆43Updated last year
• 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
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆121Updated 2 years ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆118Updated 7 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆99Updated 3 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• dinhdiep / MONOD2
  MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data
  ☆40Updated 6 years ago
• mskcc / facets
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆158Updated last week
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆98Updated last year
• bioinform / rnacocktail
  ☆89Updated 5 years ago
• XWangLabTHU / cfDNApipe
  cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
  ☆75Updated 3 years ago
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆49Updated 7 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆63Updated this week
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆136Updated last year
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆159Updated 5 months ago