Alternatives and similar repositories for cpsr

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

• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆78Updated this week
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆57Updated this week
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆52Updated 4 years ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆82Updated 11 months ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆59Updated last year
• TrinityCTAT / ctat-mutations
  Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
  ☆77Updated 3 weeks ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆102Updated last year
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆40Updated 4 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆53Updated 3 years ago
• s-andrews / BamQC
  Mapped QC analysis program
  ☆43Updated 7 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 5 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
• 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
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆64Updated last week
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 7 years ago
• Wedge-lab / battenberg
  Battenberg R package for subclonal copynumber estimation
  ☆95Updated 2 months ago
• sigven / gvanno
  Generic human DNA variant annotation pipeline
  ☆60Updated last year
• cancerit / BRASS
  Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
  ☆57Updated last year
• parklab / ShatterSeek
  ☆75Updated 2 years ago
• raphael-group / hatchet
  HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jo…
  ☆70Updated 11 months ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆74Updated 4 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆55Updated 8 months ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆54Updated last year
• genepi / nf-gwas
  A nextflow pipeline to perform state-of-the-art genome-wide association studies.
  ☆78Updated 4 months ago
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆75Updated last year
• mskilab-org / JaBbA
  MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
  ☆59Updated 10 months ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆30Updated 7 years ago
• Oshlack / Clinker
  Gene Fusion Visualiser
  ☆51Updated 3 years ago
• hartwigmedical / pipeline5
  ☆23Updated 2 months ago