Alternatives and similar repositories for CGATPipelines

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

• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• smithlabcode / methpipe
  A pipeline for analyzing DNA methylation data from bisulfite sequencing.
  ☆70Updated 3 years ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆122Updated last year
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆44Updated 7 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 4 years ago
• hartwigmedical / pipeline5
  ☆21Updated 3 weeks ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 4 years ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆57Updated 5 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
• hellbelly / BS-Snper
  ☆38Updated 4 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated last year
• 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
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆71Updated 8 months ago
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆91Updated 3 months ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆32Updated 2 years ago
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated 10 months ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 years ago
• data61 / gossamer
  Gossamer bioinformatics suite
  ☆22Updated 10 months ago
• bowhan / piPipes
  piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School
  ☆61Updated 3 months 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…
  ☆60Updated 5 years ago
• robertaboukhalil / ginkgo
  Cloud-based single-cell copy-number variation analysis tool
  ☆51Updated 2 years ago
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆36Updated 3 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆59Updated 2 weeks ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆53Updated 6 years ago
• Henikoff / Cut-and-Run
  ☆31Updated 7 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago