• SNVer

  • Referenced in 3 articles [sw36884]
  • significance of observed allele frequency against sequencing error. SNVer reports one single overall P-value ... methods. We use both simulated data and real data to demonstrate the superior performance ... feasible for analysis of whole-exome sequencing data, or even whole-genome sequencing data using...
  • svmod

  • Referenced in 1 article [sw25331]
  • Finding small somatic structural variants in exome sequencing data: a machine learning approach. Genetic variation ... several megabases. Based on recent developments in sequencing technology it has become feasable to elucidate ... related SVs with the help of sequencing data. The method uses differences in characteristics ... aims to be directly applicable for exome sequencing data to improve detection of SVs since...
  • SeqEM

  • Referenced in 1 article [sw35196]
  • unrelated individuals with next-generation sequence data, leveraging information from the sample to estimate genotype ... also apply SeqEM to exome sequence data in eight related individuals and compare the results...
  • ExomeCNV

  • Referenced in 1 article [sw35179]
  • loss of heterozygosity (LOH) from exome sequencing data extends the utility of this powerful approach ... allele frequencies, from mapped short sequence reads, and we assess both the method’s power ... apply our method to a cancer exome resequencing dataset. As expected, accuracy and resolution...
  • VarSifter

  • Referenced in 1 article [sw17296]
  • VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer. Summary: VarSifter ... quickly sort, filter, and sift through sequence variation data. A variety of filters ... simplifying visualization and analyses of exome-scale sequence variation data, this program will help bring...
  • Omics Pipe

  • Referenced in 1 article [sw26801]
  • computational framework that automates multi-omics data analysis pipelines on high performance compute clusters ... Exome-seq, Whole-Genome sequencing, ChIP-seq analyses and automatic processing of data from...
  • VarScan

  • Referenced in 7 articles [sw27471]
  • SNPs and indels) in next-generation sequencing data. The new release (VarScan 2) is implemented ... comparing the read counts. Exome-based copy number alteration detection. You can also use VarScan ... When tumor and normal undergo capture and sequencing with identical protocols, this read depth comparison...
  • Sam2bam

  • Referenced in 0 articles [sw16315]
  • speedup pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single ... systems. It can reduce the runtime of data pre-processing in marking duplicate reads ... analyzing, filtering, and converting the input data are provided by {it plug-in} tools ... about one minute for a whole-exome data set on a 16-core single-node...
  • Strelka

  • Referenced in 1 article [sw31866]
  • sample pairs. Motivation: Whole genome and exome sequencing of matched tumor–normal sample pairs ... small indel detection from sequencing data of matched tumor–normal samples. The method uses...
  • R

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

  • Referenced in 181 articles [sw03059]
  • Parallel network simulations with NEURON. The NEURON simulation...
  • Bioconductor

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

  • Referenced in 33 articles [sw04637]
  • The Rfam database is a collection of RNA...
  • Rnamotif

  • Referenced in 10 articles [sw04638]
  • The rnamotif program [1] searches a database for...
  • LIBSVM

  • Referenced in 1124 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • WEKA

  • Referenced in 292 articles [sw06435]
  • WEKA: Waikato Environment for Knowledge Analysis. WEKA is...
  • edgeR

  • Referenced in 49 articles [sw06936]
  • edgeR: a Bioconductor package for differential expression analysis...
  • Biopython

  • Referenced in 19 articles [sw07357]
  • Biopython: freely available Python tools for computational molecular...
  • minet

  • Referenced in 7 articles [sw08432]
  • minet: A R/Bioconductor Package for Inferring Large Transcriptional...
  • Spikenet

  • Referenced in 12 articles [sw08892]
  • SpikeNET: an event-driven simulation package for modelling...