Alternatives and similar repositories for cpsr

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

• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆96Updated last year
• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆69Updated last week
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆48Updated this week
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆51Updated 3 years ago
• sigven / gvanno
  Generic human DNA variant annotation pipeline
  ☆58Updated last year
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆61Updated 10 months ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 5 months ago
• Oshlack / Clinker
  Gene Fusion Visualiser
  ☆51Updated 2 years ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆60Updated 8 months ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆52Updated 3 years ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• parklab / ShatterSeek
  ☆69Updated 2 years ago
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆76Updated this week
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 2 years ago
• ncbi / BAMscale
  BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy …
  ☆70Updated 7 months ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated 11 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 2 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• Ettwiller / Damage-estimator
  Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…
  ☆53Updated 8 years ago
• TrinityCTAT / ctat-mutations
  Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
  ☆76Updated 11 months ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 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, …
  ☆46Updated 3 months ago
• cancerit / BRASS
  Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
  ☆57Updated last year
• gatk-workflows / gatk4-rnaseq-germline-snps-indels
  Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
  ☆77Updated 3 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆53Updated last month
• genepi / nf-gwas
  A nextflow pipeline to perform state-of-the-art genome-wide association studies.
  ☆69Updated 3 months ago