• DANN

  • Referenced in 1 article [sw31340]
  • learning approach for annotating the pathogenicity of genetic variants. Annotating genetic variants, especially non-coding ... variants, for the purpose of identifying pathogenic variants remains a challenge. Combined annotation-dependent depletion...
  • ExomeWalker

  • Referenced in 1 article [sw36887]
  • prioritised according to a variant score (predicted pathogenicity, rarity, pattern of variants compatible with...
  • AntigenMap 3D

  • Referenced in 1 article [sw34972]
  • applied to identify antigenic variants and vaccine strain candidates for pathogens with rapid antigenic variations...
  • VarFish

  • Referenced in 1 article [sw36001]
  • files with single or multiple samples. The variants are automatically annotated with population frequencies, molecular ... pathogenicity scores including CADD, MutationTaster, and phenotypic similarity scores. Users can filter variants based...
  • NGS

  • Referenced in 1 article [sw29692]
  • importance in the epidemiologic analysis of bacterial pathogens. However, few whole genome sequencing-based genotyping ... aureus. The SNP genotyping method calls genome variants using next-generation sequencing reads of whole ... whole genome SNP profiles and the structural variants of different isolates of methicillin-resistant ... evolution and the transmission dynamic of bacterial pathogens. The computer programs of the whole genome...
  • 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...
  • GATK

  • Referenced in 17 articles [sw12019]
  • The genome analysis toolkit: a MapReduce framework for...
  • Samtools

  • Referenced in 22 articles [sw14583]
  • Samtools is a suite of programs for interacting...
  • BLAT

  • Referenced in 36 articles [sw16891]
  • BLAT — The BLAST-Like Alignment Tool. Analyzing vertebrate...
  • FastQC

  • Referenced in 8 articles [sw16946]
  • FastQC: A quality control tool for high throughput...
  • Trimmomatic

  • Referenced in 6 articles [sw17091]
  • Trimmomatic: a flexible trimmer for Illumina sequence data...
  • IGV

  • Referenced in 3 articles [sw17276]
  • Integrative Genomics Viewer (IGV): high-performance genomics data...
  • BEDTools

  • Referenced in 11 articles [sw17302]
  • BEDTools: a flexible suite of utilities for comparing...
  • VarScan

  • Referenced in 8 articles [sw27471]
  • VarScan is a tool that detects variants (SNPs...
  • SciClone

  • Referenced in 8 articles [sw29660]
  • SciClone: inferring clonal architecture and tracking the spatial...
  • SomaticSignatures

  • Referenced in 1 article [sw36881]
  • Bioconductor/R package SomaticSignatures: Somatic Signatures - The SomaticSignatures package...
  • HitWalker

  • Referenced in 1 article [sw36882]
  • HitWalker: variant prioritization for personalized functional cancer genomics...