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
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆98Updated 4 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• asntech / QDNAseq.hg38
  QDNAseq.hg38: QDNAseq bin annotation for hg38
  ☆16Updated 2 weeks ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆31Updated 2 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆62Updated 3 months ago
• hellbelly / BS-Snper
  ☆38Updated 4 years ago
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• ikalatskaya / ISOWN
  ☆46Updated 5 years ago
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆44Updated this week
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆74Updated last year
• 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
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• s-andrews / BamQC
  Mapped QC analysis program
  ☆44Updated 7 years ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆57Updated 5 years ago
• hartwigmedical / pipeline5
  ☆21Updated 3 weeks ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆40Updated 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 5 years ago
• smithlabcode / methpipe
  A pipeline for analyzing DNA methylation data from bisulfite sequencing.
  ☆70Updated 3 years ago
• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆73Updated 2 weeks ago
• parklab / SigMA
  Mutational signature analysis for low statistics SNV data
  ☆64Updated last year
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 4 years ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆58Updated last year
• nloyfer / UXM_deconv
  ☆46Updated 2 years ago
• Clinical-Genomics / fusion-report
  Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.githu…
  ☆28Updated 4 months ago
• TrinityCTAT / ctat-mutations
  Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
  ☆78Updated last year
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• ferrannadeu / IgCaller
  Python program designed to reconstruct immunoglobulin gene rearrangements and oncogenic translocations from WGS, WES and capture NGS in l…
  ☆20Updated 2 years ago