Alternatives and similar repositories for THetA

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

• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 4 years ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆52Updated 4 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• FoundationMedicineInc / SGZ
  ☆41Updated last year
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 2 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…
  ☆53Updated 4 years ago
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated 10 months ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆71Updated 8 months ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆50Updated 3 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆83Updated 7 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆115Updated 10 months ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆106Updated last year
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆87Updated last week
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆58Updated 7 months ago
• dinhdiep / MONOD2
  MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data
  ☆39Updated 6 years ago
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆56Updated 4 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆69Updated 9 months ago
• Kennedy-Lab-UW / Duplex-Sequencing
  ☆57Updated 5 years ago
• brwnj / umitools
  Tools to handle reads sequenced with unique molecular identifiers (UMIs).
  ☆30Updated 7 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆61Updated 4 years ago
• zhou-lab / biscuit
  BISulfite-seq CUI Toolkit
  ☆65Updated 4 months ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• mskilab-org / JaBbA
  MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
  ☆57Updated 2 months ago