copy-number

There are 0 repository under copy-number topic.

• broadinstitute / ichorCNA

  Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

  copy-numberlow-coverage-sequencingcell-free-dna
  Language:R 187

• lima1 / PureCN

  Copy number calling and variant classification using targeted short read sequencing

  copy-numbercell-free-dnatumor-heterogeneitytumor-puritytumor-mutational-burdenlohbioconductor-package
  Language:R 140

• baudisgroup / segment-liftover

  Lifterover copy number segments in whole

  copy-numberliftoverprobesegmentucsc-liftover
  Language:Python 23

• ndbrown6 / MSK-GRAIL-TECHVAL

  High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants

  rcancercfdnactdnaclonal-hematopoiesiscopy-number
  Language:R 22

• gustaveroussy / EaCoN

  Easy Copy Number !

  copy-numberexome-sequencingmicroarrayrsegmentation
  Language:R 21

• polyactis / Accucopy

  Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.

  copy-numbercancer-genomicssomatic-variantsgaussian-mixture-modelsexpectation-maximizationmaximum-likelihood-estimationbayesian-information-criterionauto-correlation
  Language:C++ 17

• HenrikBengtsson / aroma.affymetrix

  🔬 R package: Analysis of Large Affymetrix Microarray Data Sets

  rpackageaffymetrixcopy-numberexpressiondnarnaanalysismicroarraylarge-scalereproducibilityhpcnotebook
  Language:R 12

• samabs / conliga

  Probabilistic inference of somatic copy number alterations using repeat DNA (FAST-SeqS)

  bayesian-methodsbayesian-inferencecopy-numbercopy-number-variationprobabilistic-modelsprobabilistic-graphical-modelsmcmcrrcpparmadillobayesian-nonparametric-modelsgenomics
  Language:C++ 9

• TNTurnerLab / CNPI

  Software for Rapid Analyses of Human Copy Number Data

  bioinformaticscopy-numbercopy-number-variationgenomegenomicsgenotypekaryotypex-chromosomey-chromosomeautosome
  Language:C++ 6

• HenrikBengtsson / CostelloPSCNSeq

  R package: Parent-specific Copy-number Estimation Pipeline using HT-Seq Data

  rht-seqcopy-number
  Language:R 3

• KrasnitzLab / CNprep

  CNprep Package - Pre-process DNA Copy Number (CN) Data for Detection of CN Events

  rr-packagecopy-number-variationcopy-numberdna-copy-numberbootstrap
  Language:R 3

• HCL-HUBL / KILDA

  KILDA (KIv2 Length Determined from a kmer Analysis) provides an alignment-free estimation of the number of KIV2 (Kringle IV type 2) repeats from FASTQ files.

  bioinformaticscopy-numberkringle
  Language:Python 1

• ndbrown6 / GAP

  Genome Alteration Print (GAP)

  rcopy-number
  Language:R 1

• adeschen / CNprep

  Processing DNA Copy Number (CN) Data for Detection of CN Events

  rr-packagedna-copy-numbercopy-number-variationcopy-numberbootstrapmodel-based-clustering
  Language:R 0

• ndbrown6 / CNtu

  Copy Number tree utilities (CNtu)

  rcopy-number
  Language:R 0

• aleighbrown / facets_snakemake

  Pipeline for running the FACETS copy number caller using Snakemake

  facetssnakemakecopy-numberpipelinecancerhtslib
  Language:R