• CNV-seq

  • Referenced in 11 articles [sw17970]
  • variation using high-throughput sequencing. Background: DNA copy number variation (CNV) has been recognized...
  • DNAcopy

  • Referenced in 7 articles [sw16252]
  • DNAcopy: DNA copy number data analysis. R package. Implements the circular binary segmentation (CBS) algorithm ... segment DNA copy number data and identify genomic regions with abnormal copy number...
  • CARAT

  • Referenced in 6 articles [sw35399]
  • novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays ... infer copy number in an allele-specific manner from high density DNA oligonuceotide arrays designed ... SNPs. Total and allele-specific copy number estimations using CARAT are independently evaluated ... algorithm are characterized using DNA samples containing differing numbers of X chromosomes as well...
  • seqCBS

  • Referenced in 6 articles [sw12152]
  • This is a method for DNA Copy Number Profiling using Next-Generation Sequencing...
  • DR-Integrator

  • Referenced in 3 articles [sw30014]
  • perform integrative analyses on paired DNA copy number and gene expression data. DR-Integrator identifies ... genes with significant correlations between DNA copy number and gene expression, and also performs ... genes with significant alterations in both DNA copy number and gene expression between two sample...
  • rSW-seq

  • Referenced in 3 articles [sw17971]
  • algorithm for detection of copy number alterations in deep sequencing data. Background: Recent advances ... variety of genomic features, including the DNA copy number profile of a cancer genome...
  • ChromoScan

  • Referenced in 3 articles [sw35412]
  • associations with disease, gene expression profiles, DNA copy number variations, as well as other genome...
  • SegAnnDB

  • Referenced in 2 articles [sw19542]
  • interactive web-based genomic segmentation. Motivation: DNA copy number profiles characterize regions of chromosome gains...
  • FLLat

  • Referenced in 2 articles [sw19127]
  • hybridization (aCGH) enables the measurement of DNA copy number across thousands of locations...
  • SeqBBS

  • Referenced in 2 articles [sw17972]
  • control samples for the study of DNA copy number variants (CNVs). In particular, the ratio...
  • DINGO

  • Referenced in 2 articles [sw29317]
  • genes found by mRNA expression, DNA copy number, methylation and microRNA expression reveal several important...
  • PurityEst

  • Referenced in 2 articles [sw24696]
  • accuracy of PurityEst compared with DNA copy number-based estimation. AVAILABILITY: PurityEst has been implemented...
  • ParticleMDI

  • Referenced in 1 article [sw35255]
  • which there are gene expression, copy number variation, DNA methylation, protein expression and microRNA data...
  • CNAmet

  • Referenced in 3 articles [sw08175]
  • CNAmet v.1.2 User Guide Copy number arrays (array CGH or SNP arrays) and expression microarrays ... cancer where the amount of genomic DNA can be linked to the amount of transcription ... DNA methylation also affects tumors in ways undetectable by an integrative analysis of copy number...
  • modENCODE

  • Referenced in 2 articles [sw22998]
  • replacement, chromatin structure, DNA replication initiation and timing, and copy number variation...
  • DNADU

  • Referenced in 2 articles [sw23315]
  • DNA sequences or genomes. It can identify periodicities, consensus repeat patterns, copy numbers and perfect ... results of using the method on different DNA sequences and genomes demonstrate efficacy and accuracy...
  • IMEx

  • Referenced in 2 articles [sw14942]
  • screen DNA sequences for microsatellites and reports the motif, copy number, genomic location, nearby genes...
  • OPTIMIZER

  • Referenced in 4 articles [sw17358]
  • makes it possible to optimize a DNA sequence using pre-computed codon usage tables from ... novelty, the tRNA gene-copy numbers. OPTIMIZER is accessible free of charge at http://genomes.urv.es...
  • THetA

  • Referenced in 3 articles [sw26927]
  • inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. Tumor samples are typically heterogeneous ... sample, for the case where copy number aberrations distinguish subpopulations. THetA successfully estimates normal admixture...
  • SegCorr

  • Referenced in 1 article [sw21050]
  • corrected for correlations possibly caused by copy number variation. The correction permitted the detection ... regions with high correlations linked to DNA methylation. Availability and implementation: R package SegCorr...