Alternatives and similar repositories for ctDNAtools

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

• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆52Updated last year
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆54Updated 4 months ago
• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆72Updated 2 months ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆61Updated 2 months ago
• ikalatskaya / ISOWN
  ☆46Updated 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 4 years ago
• hartwigmedical / pipeline5
  ☆21Updated this week
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 4 years ago
• asntech / QDNAseq.hg38
  QDNAseq bin annotation for hg38
  ☆16Updated 6 months ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 3 years ago
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• RahmanTeam / DECoN
  ☆53Updated 2 years ago
• a-xavier / tapes
  TAPES : a Tool for Assessment and Prioritisation in Exome Studies
  ☆25Updated 2 weeks ago
• jlab-code / MethylStar
  A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
  ☆35Updated 4 years ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆57Updated 5 years ago
• smithlabcode / methpipe
  A pipeline for analyzing DNA methylation data from bisulfite sequencing.
  ☆70Updated 3 years ago
• ding-lab / CharGer
  Characterization of Germline variants
  ☆98Updated 3 years ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆58Updated 11 months ago
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆43Updated this week
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆75Updated last year
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆52Updated 3 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• naumanjaved / fingerprint_maps
  Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…
  ☆28Updated last year