Alternatives and similar repositories for CNAclinic

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

• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆32Updated 2 years ago
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆25Updated 7 years ago
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆34Updated 10 years ago
• Xinglab / lr2rmats
  Long read to rMATS
  ☆32Updated 2 years ago
• hangelwen / miR-PREFeR
  microRNA PREdiction From small RNA-seq data
  ☆30Updated 8 years ago
• hellbelly / BS-Snper
  ☆39Updated 4 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• ikalatskaya / ISOWN
  ☆46Updated 6 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
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆55Updated 6 months ago
• niu-lab / msisensor-ct
  Microsatellite instability (MSI) detection for cfDNA samples.
  ☆20Updated 4 years ago
• TheJacksonLaboratory / SVE
  ☆51Updated 6 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆53Updated last year
• bjtrost / TCAG-WGS-CNV-workflow
  Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods
  ☆46Updated 3 years ago
• cortes-ciriano-lab / ReConPlot
  ☆24Updated last year
• TomSkelly / MatchAnnot
  Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.
  ☆23Updated 10 years ago
• parklab / MuSiCal
  A comprehensive toolkit for mutational signature analysis
  ☆42Updated last year
• rdemolgen / SavvySuite
  Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes
  ☆31Updated 4 months ago
• zhongw2 / GeneTEFlow
  ☆23Updated 4 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
• LappalainenLab / lorals
  ☆38Updated 2 years ago
• sartorlab / methylSig
  R package for DNA methylation analysis
  ☆19Updated last year
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 5 years ago
• 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
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆40Updated 4 years ago
• rvolden / Mandalorion-Episode-II
  Version II of Mandalorion
  ☆32Updated 6 years ago
• mskilab-org / gGnome
  R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
  ☆41Updated 3 weeks ago
• zd1 / telseq
  A software for calculating telomere length
  ☆72Updated 7 years ago
• umccr / umccrise
  DRAGEN Tumor/Normal workflow post-processing
  ☆25Updated 2 years ago
• namphuon / ViFi
  Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
  ☆30Updated 4 years ago