Alternatives and similar repositories for superFreq:

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

• UMCUGenetics / MutationalPatterns
  R package for extracting and visualizing mutational patterns in base substitution catalogues
  ☆106Updated 2 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆72Updated 3 years ago
• hbc / bcbioRNASeq
  R package for bcbio RNA-seq analysis.
  ☆62Updated 7 months ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆118Updated last year
• 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
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆53Updated 6 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆41Updated 7 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆114Updated 9 months ago
• CGATOxford / CGATPipelines
  Collection of CGAT NGS Pipelines
  ☆43Updated 6 years ago
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆145Updated 2 years ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 2 years ago
• parklab / ShatterSeek
  ☆68Updated last year
• hdng / clonevol
  Inferring and visualizing clonal evolution in multi-sample cancer sequencing
  ☆147Updated 4 years ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆96Updated last year
• mskcc / facets
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆150Updated last year
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 6 months ago
• cancerit / BRASS
  Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
  ☆57Updated 9 months ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• kundajelab / phantompeakqualtools
  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…
  ☆59Updated 4 years ago
• Nik-Zainal-Group / signature.tools.lib
  R package containing useful functions for mutational signature analysis
  ☆81Updated last week
• pmelsted / pizzly
  Fast fusion detection using kallisto
  ☆80Updated 6 months ago
• yuchaojiang / Canopy
  Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.
  ☆68Updated 3 years ago
• BIMSBbioinfo / genomation
  R package for genomic feature analysis and visualization
  ☆76Updated 3 weeks ago
• snakemake-workflows / dna-seq-varlociraptor
  A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, …
  ☆86Updated last week
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆97Updated 11 months ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• ncbi / TPMCalculator
  TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
  ☆130Updated 10 months ago
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆86Updated last month