Alternatives and similar repositories for pipeline5:

Users that are interested in pipeline5 are comparing it to the libraries listed below

• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆60Updated 4 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…
  ☆52Updated 4 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆49Updated 6 months ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆54Updated 2 years ago
• nloyfer / UXM_deconv
  ☆40Updated 2 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆56Updated 4 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 3 months ago
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated 11 months ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆38Updated 3 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆96Updated 3 years ago
• broadinstitute / PhylogicNDT
  ☆71Updated 9 months ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated last week
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 3 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆67Updated 5 months ago
• jlab-code / MethylStar
  A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
  ☆34Updated 3 years ago
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆84Updated last week
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆70Updated 4 years ago
• broadinstitute / gistic2
  Genomic Identification of Significant Targets in Cancer (GISTIC), version 2
  ☆49Updated 2 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆55Updated last week
• parklab / ShatterSeek
  ☆66Updated last year
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• ucagenomix / sicelore
  Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…
  ☆73Updated last year
• deepomicslab / SpecHLA
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …
  ☆41Updated this week
• NYU-BFX / hic-bench
  A set of pipelines for Hi-C and ChIP-Seq analysis.
  ☆46Updated 10 months ago
• AlexandrovLab / SigProfilerPlotting
  SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational pattern…
  ☆47Updated last week
• RahmanTeam / DECoN
  ☆52Updated 2 years ago
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆48Updated 6 years ago
• Henikoff / Cut-and-Run
  ☆30Updated 6 years ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆45Updated 2 years ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆108Updated 2 weeks ago