Alternatives and similar repositories for cgpBattenberg:

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

• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆70Updated 4 years ago
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆84Updated last week
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆96Updated 3 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆70Updated 8 months ago
• Nik-Zainal-Group / signature.tools.lib
  R package containing useful functions for mutational signature analysis
  ☆80Updated this week
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆60Updated 2 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆52Updated 5 years ago
• arq5x / bedtools-protocols
  ☆78Updated 10 years ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆117Updated last year
• hbc / bcbioRNASeq
  R package for bcbio RNA-seq analysis.
  ☆59Updated 5 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…
  ☆56Updated 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
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆96Updated 2 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆72Updated 3 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 3 months ago
• CGATOxford / CGATPipelines
  Collection of CGAT NGS Pipelines
  ☆43Updated 6 years ago
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆56Updated 3 years ago
• parklab / ShatterSeek
  ☆66Updated 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.
  ☆48Updated 5 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 3 months ago
• hdng / clonevol
  Inferring and visualizing clonal evolution in multi-sample cancer sequencing
  ☆147Updated 4 years ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆70Updated 5 months ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆65Updated 4 years ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆60Updated 4 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆57Updated 5 months ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆67Updated last month