eyzhao / hrdetect-pipeline

Related projects ⓘ

Alternatives and complementary repositories for hrdetect-pipeline

• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆27Updated last year
• FJD-CEPH / aCNViewer
  Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
  ☆28Updated 5 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆29Updated last year
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated last month
• caravagnalab / mobster
  Model-based subclonal deconvolution from bulk sequencing.
  ☆33Updated last year
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆37Updated last year
• QingliGuo / FFPEsig
  Codes and Data for FFPEsig manuscript
  ☆15Updated 9 months ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• kgori / sigfit
  Flexible Bayesian inference of mutational signatures
  ☆33Updated last year
• cancerit / alleleCount
  Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…
  ☆43Updated 2 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆69Updated 5 months ago
• smshuai / DriverPower
  DriverPower
  ☆26Updated 4 months ago
• TRON-Bioinformatics / EasyFuse
  EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
  ☆50Updated 2 weeks ago
• zhouzilu / iCNV
  Integrated copy number variation detection toolset
  ☆25Updated 4 years ago
• carjed / helmsman
  highly-efficient & lightweight mutation signature matrix aggregation
  ☆19Updated 2 years ago
• ait5 / CNApp
  CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-frien…
  ☆18Updated 4 years ago
• getzlab / MutSig2CV
  MutSig2CV from Lawrence et al. 2014
  ☆30Updated 4 years ago
• sfu-compbio / citup
  Clonality Inference in Multiple Tumor Samples using Phylogeny
  ☆13Updated 9 years ago
• amcpherson / citup
  Clonality inference in multiple tumor samples using phylogeny
  ☆13Updated 7 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆59Updated 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 …
  ☆33Updated 4 months ago
• markowetzlab / CINSignatureQuantification
  Quantifying copy number signatures from absolute copy number profiles
  ☆23Updated 3 weeks ago
• umccr / vcf_stuff
  📊Evaluating, filtering, comparing, and visualising VCF
  ☆27Updated last year
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆27Updated last year
• mskcc / facets-suite
  Utility functions for FACETS
  ☆34Updated 7 months ago
• cancer-genomics / reproduce_lucas_wflow
  ☆25Updated 8 months ago
• nghiavtr / FuSeq
  ☆32Updated 2 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆41Updated 2 years ago