Alternatives and similar repositories for PanCanAtlasGermline:

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

• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated 11 months ago
• getzlab / MutSig2CV
  MutSig2CV from Lawrence et al. 2014
  ☆31Updated 4 years ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆61Updated 4 years ago
• broadinstitute / gistic2
  Genomic Identification of Significant Targets in Cancer (GISTIC), version 2
  ☆51Updated 3 years ago
• aeeckhou / shallowHRD
  This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …
  ☆34Updated 9 months ago
• icbi-lab / Immunophenogram
  ☆40Updated 7 years ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• jason-weirather / hla-polysolver
  Fork of the Polysolver project
  ☆31Updated 5 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆27Updated 2 years ago
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• KarchinLab / 2020plus
  Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
  ☆49Updated 9 months ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆30Updated last year
• broadinstitute / RNA_MUTECT_1.0-1
  ☆38Updated 5 years ago
• jmzeng1314 / cnv
  ☆32Updated 7 years ago
• parklab / SigMA
  Mutational signature analysis for low statistics SNV data
  ☆63Updated 8 months ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆39Updated last year
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• mskcc / facets-suite
  Utility functions for FACETS
  ☆35Updated last year
• OpenGene / ctdna-pipeline
  A simplified pipeline for ctDNA sequencing data analysis
  ☆36Updated 7 years ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆58Updated 8 months ago
• Bioconductor / copy-number-analysis
  Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis
  ☆21Updated 2 years ago
• ShixiangWang / Variants2Neoantigen
  A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
  ☆29Updated 5 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 4 years ago
• davetang / defining_genomic_regions
  Define regions in the genome
  ☆30Updated 3 years ago
• icbi-lab / nextNEOpi
  nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
  ☆73Updated last week
• reiterlab / treeomics
  Decrypting somatic mutation patterns to reveal the evolution of cancer
  ☆56Updated 4 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆42Updated 3 years ago