Alternatives and similar repositories for SECNVs

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

• FoundationMedicineInc / SGZ
  ☆43Updated last year
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 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 4 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆110Updated last year
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆51Updated last year
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆61Updated last month
• OSU-SRLab / MANTIS
  Microsatellite Analysis for Normal-Tumor InStability
  ☆74Updated 3 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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
• OpenGene / ctdna-pipeline
  A simplified pipeline for ctDNA sequencing data analysis
  ☆37Updated 8 years ago
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆102Updated last month
• sztup / scarHRD
  ☆116Updated 2 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆136Updated last year
• xjtu-omics / msisensor-pro
  Microsatellite Instability (MSI) detection using high-throughput sequencing data.
  ☆111Updated 5 months ago
• RahmanTeam / DECoN
  ☆53Updated 2 years ago
• Genotek / ClassifyCNV
  ClassifyCNV: a tool for clinical annotation of copy-number variants
  ☆66Updated 2 years ago
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆91Updated 2 months ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆44Updated 7 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆85Updated 7 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆147Updated 2 weeks ago
• hartwigmedical / pipeline5
  ☆21Updated 2 weeks ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• VUmcCGP / wisecondor
  WISECONDOR (WIthin-SamplE COpy Number aberration DetectOR): Detect fetal trisomies and smaller CNV's in a maternal plasma sample using wh…
  ☆46Updated last year
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• aeeckhou / shallowHRD
  This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …
  ☆34Updated last week
• Kennedy-Lab-UW / Duplex-Seq-Pipeline
  A standalone end-to-end data analysis pipeline for Duplex Sequencing
  ☆20Updated last year
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• dieterich-lab / DCC
  DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies …
  ☆37Updated 3 years ago