Alternatives and similar repositories for SVclone

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

• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆30Updated 11 months ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆32Updated 10 months ago
• 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…
  ☆44Updated 3 years ago
• eyzhao / hrdetect-pipeline
  ☆36Updated 6 years ago
• caravagnalab / mobster
  Model-based tumour subclonal deconvolution using population genetics
  ☆34Updated 2 months ago
• FJD-CEPH / aCNViewer
  Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
  ☆29Updated 6 years ago
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆42Updated 2 years ago
• mskilab-org / dryclean
  Irons out wrinkles in noisy coverage data using robust PCA
  ☆15Updated 8 months ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆32Updated 2 years ago
• parklab / MuSiCal
  A comprehensive toolkit for mutational signature analysis
  ☆41Updated last year
• smshuai / DriverPower
  DriverPower
  ☆26Updated last year
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆72Updated last year
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆28Updated 2 years ago
• morrislab / TrackSig
  A framework to infer mutational signatures in cancer over time
  ☆56Updated 6 years ago
• morrislab / pairtree
  Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…
  ☆42Updated last year
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 7 years ago
• PeeperLab / CopywriteR
  DNA copy number detection from off-target sequence data
  ☆33Updated 7 years ago
• QingliGuo / FFPEsig
  Codes and Data for FFPEsig manuscript
  ☆17Updated 2 years ago
• ChrisMaherLab / ClonEvol
  ☆13Updated 8 years ago
• thelovelab / rnaseqDTU
  RNA-seq workflow: differential transcript usage
  ☆23Updated 2 years ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆65Updated 5 years ago
• kgori / sigfit
  Flexible Bayesian inference of mutational signatures
  ☆41Updated 3 years ago
• mbourgey / EBI_cancer_workshop_CNV
  hands-on for NGS/SNParray CNV call trainning
  ☆20Updated 3 years ago
• chrisamiller / copyCat
  a parallel R package for detecting copy-number alterations from short sequencing reads
  ☆23Updated 4 years ago
• gtrichard / deepStats
  deepStats: a stastitical toolbox for deeptools and genomic signals
  ☆35Updated 4 years ago
• slagtermaarten / LOHHLA
  Fork of https://bitbucket.org/mcgranahanlab/lohhla
  ☆18Updated 5 years ago
• umccr / umccrise
  DRAGEN Tumor/Normal workflow post-processing
  ☆25Updated 2 years ago
• biosinodx / SCcaller
  Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
  ☆35Updated last year
• hellbelly / BS-Snper
  ☆39Updated 4 years ago
• dnaase / Bis-tools
  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…
  ☆32Updated 4 years ago