Alternatives and similar repositories for oncotator

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

• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 years ago
• griffithlab / pVAC-Seq
  DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
  ☆61Updated 6 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆62Updated 3 years ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆53Updated 3 years ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆58Updated last year
• Kennedy-Lab-UW / Duplex-Sequencing
  ☆57Updated 5 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆98Updated 4 years ago
• FoundationMedicineInc / SGZ
  ☆43Updated last year
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆52Updated 3 years ago
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 9 years ago
• ding-lab / CharGer
  Characterization of Germline variants
  ☆98Updated 3 years ago
• ikalatskaya / ISOWN
  ☆46Updated 5 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆63Updated 3 months ago
• soccin / BIC-variants_pipeline
  BIC@MSKCC Variants Pipeline
  ☆24Updated 2 years ago
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 5 years 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…
  ☆55Updated 5 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• OSU-SRLab / MANTIS
  Microsatellite Analysis for Normal-Tumor InStability
  ☆76Updated 3 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 4 years ago
• OpenGene / ctdna-pipeline
  A simplified pipeline for ctDNA sequencing data analysis
  ☆37Updated 8 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆75Updated last year
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 5 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆52Updated last year