• affy

  • Referenced in 35 articles [sw08345]
  • Package for Analyses of Affymetrix Oligonucleotide Arrays. We describe an extensible, interactive environment for data ... analysis and exploration of Affymetrix oligonucleotide array probe-level data. The software utilities provided with...
  • oligo

  • Referenced in 9 articles [sw06102]
  • package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files...
  • Affycomp III

  • Referenced in 11 articles [sw14610]
  • Measures. Motivation: The defining feature of oligonucleotide expression arrays is the use of several probes...
  • CARAT

  • Referenced in 6 articles [sw35399]
  • copy number changes using high density oligonucleotide arrays. Results: We describe a novel algorithm called...
  • affycomp

  • Referenced in 3 articles [sw10463]
  • compare expression measures for Affymetrix Oligonucleotide Arrays...
  • dChip

  • Referenced in 3 articles [sw08350]
  • implementing model-based expression analysis of oligonucleotide arrays and several high-level analysis procedures...
  • affyPara

  • Referenced in 1 article [sw11306]
  • affyPara: Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays. R package. The package contains parallelized functions ... exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data...
  • panp

  • Referenced in 3 articles [sw30032]
  • Method of Gene Detection on Oligonucleotide Expression Arrays...
  • logitT

  • Referenced in 1 article [sw20388]
  • test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi...
  • dChipSNP

  • Referenced in 6 articles [sw18745]
  • clustering of SNP-array-based loss-of-heterozygosity. Motivation: Oligonucleotide microarrays allow genotyping of thousands ... report automated methods for pooling SNP array replicates to make LOH calls, visualizing...
  • tilingArray

  • Referenced in 1 article [sw25752]
  • tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays. The package provides functionality that...
  • CGHPRO

  • Referenced in 1 article [sw07373]
  • reference DNA onto arrays of genomic BAC clones, cDNAs or oligonucleotides, and after correction ... dosage from raw signal intensities obtained by array CGH experiments, and which does not depend...
  • xMAN

  • Referenced in 1 article [sw35339]
  • genome of any length. By converting oligonucleotides to integers hashed in RAM, xMAN can scan ... Affymetrix whole human genome tiling arrays to the entire genome in less than ... chip experiment on whole human genome tiling arrays. Those improvements were confirmed by direct ChIP ... other high-throughput genomic technologies for oligonucleotide mapping...
  • fREDUCE

  • Referenced in 2 articles [sw35521]
  • refinements that allow efficient exhaustive searches of oligonucleotides with a specified number of degenerate IUPAC ... degenerate transcription factor binding sites, especially from array datasets with weak signals that may elude...
  • ICEP

  • Referenced in 1 article [sw23747]
  • gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors ... easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree...
  • R

  • Referenced in 8873 articles [sw00771]
  • R is a language and environment for statistical...
  • STAR

  • Referenced in 13 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • S-PLUS

  • Referenced in 604 articles [sw02892]
  • S-PLUS is a powerful environment for statistical...
  • AMPL

  • Referenced in 602 articles [sw04001]
  • AMPL is a comprehensive and powerful algebraic modeling...
  • CPLEX

  • Referenced in 2641 articles [sw04082]
  • IBM® ILOG® CPLEX® offers C, C++, Java, .NET...