Alternatives and similar repositories for CODEX2

Users that are interested in CODEX2 are comparing it to the libraries listed below

• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• sdchandra / CNAclinic
  ☆26Updated last year
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 3 years ago
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆34Updated 6 years ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 3 years ago
• s-andrews / BamQC
  Mapped QC analysis program
  ☆44Updated 7 years ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 9 years ago
• pughlab / bamgineer
  Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
  ☆37Updated 5 years ago
• nghiavtr / FuSeq
  ☆33Updated 3 years ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• pmelsted / pizzly
  Fast fusion detection using kallisto
  ☆79Updated 4 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…
  ☆45Updated 3 years ago
• Clinical-Genomics / fusion-report
  Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.githu…
  ☆28Updated 4 months ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆55Updated 4 months ago
• LosicLab / starchip
  Detection of Circular RNA and Fusions from RNA-Seq
  ☆32Updated 7 years ago
• WGLab / SeqMule
  Automated human exome/genome variants detection from FASTQ files
  ☆23Updated 4 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• ikalatskaya / ISOWN
  ☆46Updated 5 years ago
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆36Updated 3 years ago
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 5 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated 2 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆25Updated 7 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆31Updated 2 years ago
• brwnj / umitools
  Tools to handle reads sequenced with unique molecular identifiers (UMIs).
  ☆30Updated 8 years ago
• hellbelly / BS-Snper
  ☆38Updated 4 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated last year
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆98Updated last year