Alternatives and similar repositories for vdjviz

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

• pdxgx / neoepiscope
  predicts neoepitopes from phased somatic mutations detected using tumor/normal DNA-seq data
  ☆27Updated last year
• ChrisMaherLab / INTEGRATE-Neo
  ☆19Updated 7 years ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated 2 months ago
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆30Updated 6 years ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• maxplanck-ie / rna-seq-qc
  Rna-seq pipeline, From FASTQ to differential expression analysis...
  ☆20Updated 8 years ago
• ambj / MuPeXI
  MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.
  ☆50Updated 5 years ago
• PGDX / cerebro-paper
  ☆23Updated 6 years ago
• ndbrown6 / MSK-GRAIL-TECHVAL
  High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
  ☆22Updated 5 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆50Updated 3 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• yuchaojiang / MARATHON
  Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny
  ☆20Updated 5 years ago
• khuranalab / CompositeDriver
  Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
  ☆15Updated 6 years ago
• vanallenlab / retained-intron-neoantigen-pipeline
  Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
  ☆28Updated 4 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆31Updated last year
• umccr / vcf_stuff
  📊Evaluating, filtering, comparing, and visualising VCF
  ☆28Updated 2 years ago
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆34Updated 4 years ago
• eyzhao / hrdetect-pipeline
  ☆34Updated 5 years ago
• PeeperLab / CopywriteR
  DNA copy number detection from off-target sequence data
  ☆32Updated 7 years ago
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆41Updated 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…
  ☆45Updated 2 years ago
• biosinodx / SCcaller
  Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
  ☆34Updated 6 months ago
• mehdiborji / nanoranger
  simplified cellranger for long-read data
  ☆19Updated last month
• FJD-CEPH / aCNViewer
  Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
  ☆29Updated 6 years ago
• jrflab / modules
  MSKCC Reis-Filho Lab pipeline thingy
  ☆17Updated 3 weeks ago
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 4 years ago
• mandricigor / imrep
  ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.
  ☆28Updated 5 years ago
• KChen-lab / MonoVar
  Single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data
  ☆12Updated 5 years ago
• morrislab / pairtree
  Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…
  ☆37Updated last year