• dChipSNP

  • Referenced in 6 articles [sw18745]
  • dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity. Motivation: Oligonucleotide microarrays ... report automated methods for pooling SNP array replicates to make LOH calls, visualizing...
  • VanillaICE

  • Referenced in 6 articles [sw11310]
  • characterizing chromosomal alterations in high throughput SNP arrays. Background (http://www.biostat.jhsph.edu/ iruczins/software/vanillaice.html): High density single ... diseases are linked to such chromosomal alterations, SNP chips promise new insights for these diseases ... fitting hidden Markov models on genomic array data to infer chromosomal alterations, including deletions, amplifications...
  • PLASQ

  • Referenced in 6 articles [sw18746]
  • allelic dosage in cancer cells from SNP array data. Human cancer is largely driven ... cancer cells from single-nucleotide polymorphism (SNP) microarray data. Our approach is based upon ... novel classification of probes on the array. As a result of this classification ... cancer samples (e.g., CCCCT at an amplified SNP). Our approach is illustrated on a variety...
  • CNAmet

  • Referenced in 3 articles [sw08175]
  • Copy number arrays (array CGH or SNP arrays) and expression microarrays form an essential part...
  • Rseg

  • Referenced in 1 article [sw21161]
  • package to optimize segmentation of SNP array data. The use of high-density SNP arrays...
  • snpQC

  • Referenced in 1 article [sw17243]
  • pipeline for quality control of Illumina SNP genotyping array data. In genome-wide association studies ... perform QC analyses of Illumina SNP array data. It applies a wide range of common...
  • SNPchip

  • Referenced in 1 article [sw11311]
  • SNPchip: R classes and methods for SNP array data. Summary: High-density single nucleotide polymorphism...
  • SeqEM

  • Referenced in 1 article [sw35196]
  • results to genotypes from an Illumina SNP array, showing that SeqEM behaves well in real...
  • CARAT

  • Referenced in 6 articles [sw35399]
  • specific manner from high density DNA oligonuceotide arrays designed to genotype over 100, 000 SNPs ... output. When coupled with SNP genotype calls from the same array, CARAT provides additional detail...
  • GenoSNP

  • Referenced in 4 articles [sw34351]
  • single nucleotide polymorphism (SNP) by SNP basis. This approach assumes the availability of a large ... same array and platform. We have developed a SNP genotyping algorithm for the Illumina Infinium...
  • humarray

  • Referenced in 0 articles [sw15969]
  • chip ids to rs-ids for SNP-arrays. Retrieval of chromosome and position for gene...
  • dartR

  • Referenced in 1 article [sw38558]
  • that facilitate the import and analysis of SNP (single nucleotide polymorphism) and silicodart (presence/absence) data ... data generated by DarT (Diversity Arrays Technology). However, once SNP or related fragment presence/absence data...
  • SNPMaP

  • Referenced in 1 article [sw32712]
  • studies using thousands of high-density SNP microarrays are becoming an essential tool ... arrays. We present a set of software tools for processing SNPMaP (SNP microarrays and pooling...
  • 2SNP

  • Referenced in 1 article [sw17193]
  • 2SNP: Scalable Phasing Based on 2-SNP Haplotypes. Summary: 2SNP software package implements ... long genome sequences, e.g. obtained from DNA arrays. As an input 2SNP takes genotype matrix...
  • R

  • Referenced in 8836 articles [sw00771]
  • R is a language and environment for statistical...
  • STAR

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

  • Referenced in 308 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • oligo

  • Referenced in 9 articles [sw06102]
  • (R) A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon...
  • SAS

  • Referenced in 1515 articles [sw06377]
  • SAS (Statistical Analysis System) is an integrated system...