Alternatives and similar repositories for phylowgs

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

• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 5 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆109Updated 5 years ago
• reiterlab / treeomics
  Decrypting somatic mutation patterns to reveal the evolution of cancer
  ☆56Updated 4 years ago
• ratschlab / spladder
  Tool for the detection and quantification of alternative splicing events from RNA-Seq data.
  ☆111Updated 6 months ago
• parklab / ShatterSeek
  ☆73Updated 2 years ago
• griffithlab / pVAC-Seq
  DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
  ☆61Updated 6 years ago
• broadinstitute / mutect
  MuTect -- Accurate and sensitive cancer mutation detection
  ☆102Updated 2 years ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆121Updated 2 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 5 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆100Updated 4 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆53Updated 6 years ago
• hdng / clonevol
  Inferring and visualizing clonal evolution in multi-sample cancer sequencing
  ☆148Updated 5 years ago
• TrinityCTAT / ctat-mutations
  Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
  ☆77Updated 2 weeks ago
• taylor-lab / hotspots
  Identifying recurrent mutations in cancer
  ☆39Updated 4 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• zhou-lab / biscuit
  BISulfite-seq CUI Toolkit
  ☆70Updated 3 months ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• nellore / intropolis
  Exon-exon splice junctions across SRA
  ☆43Updated 4 years ago
• raphael-group / THetA
  Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberration…
  ☆75Updated 4 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 years ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Updated 5 years ago
• bmvdgeijn / WASP
  WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
  ☆110Updated 4 years ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 3 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆117Updated last year
• CGATOxford / cgat
  Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
  ☆124Updated 7 years ago
• thelovelab / tximport
  Transcript quantification import for modular pipelines
  ☆143Updated 3 months ago
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆95Updated last month
• 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
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆118Updated 7 years ago
• yarden / MISO
  MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
  ☆137Updated 3 years ago