• PCAP

  • Referenced in 3 articles [sw17185]
  • missing overlaps caused by sequencing errors. Repetitive regions of reads are detected on the basis...
  • abSNP

  • Referenced in 1 article [sw33988]
  • abSNP: RNA-Seq SNP calling in repetitive regions via abundance estimation. Variant calling, in particular ... able to successfully make calls on repetitive gene regions by exploiting the quality scores ... different genes, in order to identify which repetitive copy a particular read is sampled from ... method offers significant performance gains on repetitive regions in simulated data. In particular, the algorithm...
  • Ragout

  • Referenced in 1 article [sw23971]
  • help assemblers resolve ambiguities in repetitive regions of the genome. However, their popularity in contemporary...
  • dipSPAdes

  • Referenced in 2 articles [sw19477]
  • advantage of divergence between haplomes in repetitive genome regions to resolve them and construct longer...
  • Kangaroo

  • Referenced in 3 articles [sw38272]
  • used to identify short repetitive DNA sequences in human coding regions for the purpose...
  • CloudRS

  • Referenced in 0 articles [sw34375]
  • when dealing with reads from repetitive regions. We also illustrate several probabilistic measures we introduce...
  • Sniper

  • Referenced in 1 article [sw33991]
  • primarily because of redundant genomic regions, such as interspersed repetitive elements and paralogous genes, present...
  • PICS

  • Referenced in 3 articles [sw37329]
  • Probabilistic Inference for ChIP-seq) for identifying regions bound by transcription factors from aligned reads ... repetitiveness. It estimates uncertainties in model parameters that can be used to define confidence regions...
  • BISMA

  • Referenced in 2 articles [sw23507]
  • analysis of individual clones from unique and repetitive sequences. Background: Bisulfite sequencing is a popular ... methylation patterns at high resolution. A region of interest is targeted by PCR and about ... supports for the first time analysis of repetitive sequences. Conclusions: BISMA works highly automated...
  • PipMaker

  • Referenced in 8 articles [sw17257]
  • features such as exons of genes and repetitive elements, and colors can be used ... that can be inferred (e.g., protein-coding regions andcis-regulatory elements) depend on the level...
  • Maple

  • Referenced in 5363 articles [sw00545]
  • The result of over 30 years of cutting...
  • Mathematica

  • Referenced in 6337 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 13460 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 9810 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 1970 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • Scilab

  • Referenced in 173 articles [sw00834]
  • Scilab includes hundreds of mathematical functions. It has...
  • MACSYMA

  • Referenced in 720 articles [sw01209]
  • Macsyma is a general purpose symbolic-numerical-graphical...
  • STAR

  • Referenced in 15 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • SeDuMi

  • Referenced in 1272 articles [sw04002]
  • SeDuMi is a Matlab toolbox for solving optimization...
  • SDPT3

  • Referenced in 697 articles [sw04009]
  • This software is designed to solve conic programming...