Alternatives and similar repositories for citup

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

• ChrisMaherLab / ClonEvol
  ☆13Updated 8 years ago
• jason-weirather / hla-polysolver
  Fork of the Polysolver project
  ☆33Updated 6 years ago
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆42Updated 2 years ago
• davetang / defining_genomic_regions
  Define regions in the genome
  ☆33Updated 3 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆72Updated last year
• biosinodx / SCcaller
  Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
  ☆35Updated last year
• 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
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆65Updated 5 years ago
• ChrisMaherLab / INTEGRATE-Neo
  ☆19Updated 7 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆31Updated 9 months ago
• cancersysbio / SCIMET
  Spatial Computational Inference of MEtastatic Timing (SCIMET)
  ☆14Updated 6 years ago
• gxiaolab / REDITs
  RNA editing tests
  ☆17Updated 5 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆32Updated 2 years ago
• hartwigmedical / pipeline5
  ☆21Updated last month
• huishenlab / biscuit
  BISulfite-seq CUI Toolkit
  ☆25Updated 2 weeks ago
• parklab / MuSiCal
  A comprehensive toolkit for mutational signature analysis
  ☆42Updated last year
• deepomicslab / SpecHLA
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …
  ☆51Updated 2 months ago
• KhiabanianLab / All-FIT
  All-FIT - Allele-Frequency-based Imputation of Tumor Purity
  ☆18Updated 6 years ago
• aeeckhou / shallowHRD
  This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …
  ☆35Updated 3 months ago
• zhqingit / giremi
  GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
  ☆44Updated 8 years ago
• hellbelly / BS-Snper
  ☆39Updated 4 years ago
• tbischler / PEAKachu
  Peak calling tool for CLIP-seq data
  ☆14Updated 4 years ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• a2iEditing / RNAEditingIndexer
  A tool for the calculation of RNA-editing index for RNA seq data
  ☆45Updated last month
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆30Updated 10 months ago
• TRON-Bioinformatics / EasyFuse
  EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.
  ☆62Updated 2 months ago
• kundajelab / ataqc
  ☆17Updated 6 years ago
• broadinstitute / PhylogicNDT
  ☆82Updated 8 months ago
• cran / sequenza
   This is a read-only mirror of the CRAN R package repository. sequenza — Copy Number Estimation from Tumor Genome Sequencing Data. Homep…
  ☆20Updated 6 years ago