raphael-group / THetA

Related projects ⓘ

Alternatives and complementary repositories for THetA

• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆69Updated 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
  ☆94Updated 3 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• humanlongevity / HLA
  xHLA: Fast and accurate HLA typing from short read sequence data
  ☆104Updated last year
• griffithlab / pVAC-Seq
  DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
  ☆61Updated 5 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆96Updated 2 years ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆115Updated last year
• felixfan / PyHLA
  Python for HLA analysis: summary, association analysis, zygosity test and interaction test
  ☆32Updated 3 months ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆69Updated 2 months ago
• FoundationMedicineInc / SGZ
  ☆38Updated 9 months ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆49Updated 2 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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…
  ☆76Updated 4 years ago
• broadinstitute / PhylogicNDT
  ☆70Updated 6 months ago
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆55Updated 3 years ago
• arq5x / bedtools-protocols
  ☆78Updated 10 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆82Updated 6 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆94Updated 6 months ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆45Updated 6 years ago
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆83Updated last week
• 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…
  ☆50Updated 4 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆60Updated 2 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.
  ☆48Updated 5 years ago
• broadinstitute / oncotator
  ☆67Updated 2 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆69Updated 5 months ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆52Updated 5 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆111Updated 4 months ago
• hbc / bcbioRNASeq
  R package for bcbio RNA-seq analysis.
  ☆58Updated 2 months ago
• Ettwiller / Damage-estimator
  Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…
  ☆51Updated 7 years ago