Alternatives and similar repositories for LOHHLA:

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

• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆39Updated last year
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• FJD-CEPH / aCNViewer
  Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
  ☆29Updated 5 years ago
• sfu-compbio / citup
  Clonality Inference in Multiple Tumor Samples using Phylogeny
  ☆14Updated 9 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…
  ☆19Updated 5 years ago
• navinlabcode / ACT_paper
  Scripts used for the ACT paper
  ☆12Updated 3 years ago
• KhiabanianLab / All-FIT
  All-FIT - Allele-Frequency-based Imputation of Tumor Purity
  ☆17Updated 5 years ago
• amcpherson / citup
  Clonality inference in multiple tumor samples using phylogeny
  ☆13Updated 7 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆30Updated last year
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated this week
• nriddiford / cnvPlotteR
  Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec
  ☆13Updated 4 years ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 3 years ago
• henssenlab / TreeShapedRearrangements
  Code and data from Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020)
  ☆15Updated 4 years ago
• Niinleslie / MesKit
  A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations
  ☆35Updated 3 years ago
• yuchaojiang / SCALE
  Allele-Specific Expression by Single-Cell RNA Sequencing
  ☆28Updated 4 years ago
• biosinodx / SCcaller
  Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
  ☆34Updated 4 months ago
• AlexandrovLab / SigProfilerTopography
  SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA re…
  ☆19Updated last month
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆28Updated last month
• gersteinlab / FunSeq2
  A flexible framework to annotate and prioritize cancer somatic mutations.
  ☆8Updated 7 years ago
• khuranalab / CompositeDriver
  Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
  ☆15Updated 6 years ago
• cancer-genomics / reproduce_lucas_wflow
  ☆28Updated last year
• mskcc / facets-suite
  Utility functions for FACETS
  ☆34Updated last year
• kundajelab / ataqc
  ☆16Updated 6 years ago
• AlexandrovLab / SigProfilerClusters
  Tool for analyzing the inter-mutational distances between SNV-SNV and INDEL-INDEL mutations. Tool separates mutations into clustered and …
  ☆12Updated this week
• parklab / MSIprofiler
  Repo that aids in the detection of microsatellite instabilities (MSI) from sequencing data
  ☆20Updated 11 months ago
• amf71 / cloneMap
  An R package to plot maps of clone distributions in somatic evolution
  ☆17Updated last year
• zhiyhu / NMD-paper
  A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay
  ☆14Updated 4 years ago
• PoisonAlien / somaticfreq
  knowledge-based genotyping of cancer hotspots from the tumor BAM files
  ☆21Updated 3 years ago
• hanasusak / cDriver
  cDriver R package for finding candidate driver genes in cancers
  ☆18Updated 7 years ago
• smshuai / DriverPower
  DriverPower
  ☆26Updated 2 months ago