• PLINK

  • Referenced in 66 articles [sw04581]
  • open-source whole genome association analysis toolset, designed to perform a range of basic, large...
  • Minfi

  • Referenced in 6 articles [sw23478]
  • loci across a range of genomic features. Although less comprehensive than high-throughput sequencing-based...
  • BWA

  • Referenced in 51 articles [sw34374]
  • large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack ... while the rest two for longer sequences ranged from 70bp to 1Mbp...
  • AVID

  • Referenced in 11 articles [sw17110]
  • method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions...
  • SummarizedExperiment

  • Referenced in 2 articles [sw41943]
  • other mode. The rows typically represent genomic ranges of interest and the columns represent samples...
  • consensusSeekeR

  • Referenced in 1 article [sw22388]
  • experiences using genomic positions and genomic ranges. This package compares genomic positions and genomic ranges...
  • SSRscanner

  • Referenced in 1 article [sw14825]
  • markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping ... assisted selection of crop plants and a range of molecular ecology and diversity studies. These ... distributed almost at random throughout the genome, ranging from mononucleotide to trinucleotide repeats. They ... exact location of each SSR in the genome. SSRscanner is user friendly. It can search...
  • PseKNC

  • Referenced in 31 articles [sw22436]
  • order information, particularly the global or long-range sequence order information, via the physicochemical properties ... dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different...
  • ARACNE

  • Referenced in 38 articles [sw17200]
  • successful only for lower eukaryotes with simple genomes. Here we present ARACNE, a novel algorithm ... general enough to address a wider range of network deconvolution problems. This method uses...
  • BEDOPS

  • Referenced in 1 article [sw17305]
  • Operating on Genomic Ranges Using BEDOPS. The bulk of modern genomics research includes, in part...
  • XMRF

  • Referenced in 5 articles [sw22303]
  • Markov Networks to a wide range of high-throughput genomics data...
  • GenomicTuples

  • Referenced in 1 article [sw29183]
  • analogous to those available for genomic ranges in the GenomicRanges Bioconductor package...
  • MultiAssayExperiment

  • Referenced in 1 article [sw41944]
  • individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • software environment for whole-cell simulation. MOTIVATION: Genome sequencing projects and further systematic functional analyses ... mass of molecular information for a wide range of model organisms. This provides us with ... smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR...
  • MetaGeneAnnotator

  • Referenced in 3 articles [sw17338]
  • transferred and prophage genes in a prokaryotic genome. In this paper, we also propose ... expedite wide ranges of microbial genome studies, such as genome annotations and metagenome analyses...
  • sparsebn

  • Referenced in 2 articles [sw21046]
  • important problem with wide applications, ranging from genomics to the social sciences. Nowadays datasets typically...
  • cmenet

  • Referenced in 8 articles [sw21048]
  • wide range of applications in engineering, social sciences and genomics. The challenge in model selection...
  • MENDEL

  • Referenced in 7 articles [sw14990]
  • gene mapping methods, ranging from parametric linkage in large pedigrees to genome-wide association with ... easier to use and has a wider range of applications. Supported platforms include Linux, MacOS...
  • GOLD

  • Referenced in 6 articles [sw23027]
  • Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs ... diverse range of Sequencing Projects (such as isolate genome, single-cell genome, metagenome, metatranscriptome...
  • PPS

  • Referenced in 3 articles [sw18337]
  • thus capture true hidden periodicities in genomes. In addition, performance tests indicate that ... method may have a broad range of applications in genomic analysis. The MATLAB programs...