Alternatives and similar repositories for MuSiC2

Users that are interested in MuSiC2 are comparing it to the libraries listed below

• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• ikalatskaya / ISOWN
  ☆46Updated 5 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆51Updated 3 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
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆60Updated 10 months ago
• CGATOxford / CGATPipelines
  Collection of CGAT NGS Pipelines
  ☆43Updated 6 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆61Updated 3 weeks ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 4 years ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆44Updated 7 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
• aeeckhou / shallowHRD
  This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …
  ☆34Updated last year
• soccin / BIC-variants_pipeline
  BIC@MSKCC Variants Pipeline
  ☆24Updated 2 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• smithlabcode / methpipe
  A pipeline for analyzing DNA methylation data from bisulfite sequencing.
  ☆70Updated 2 years ago
• bjtrost / TCAG-WGS-CNV-workflow
  Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods
  ☆46Updated 2 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated last year
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 9 years ago
• Bioconductor / copy-number-analysis
  Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis
  ☆20Updated 2 years ago
• hartwigmedical / pipeline5
  ☆21Updated last week
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆74Updated 11 months ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• dnaase / Bis-tools
  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…
  ☆32Updated 3 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
• 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.
  ☆49Updated 6 years ago
• ding-lab / CharGer
  Characterization of Germline variants
  ☆98Updated 3 years ago
• NYU-BFX / hic-bench
  A set of pipelines for Hi-C and ChIP-Seq analysis.
  ☆47Updated last year
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago