• Bioconductor

  • Referenced in 320 articles [sw04205]
  • analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language...
  • Cytoscape

  • Referenced in 82 articles [sw09080]
  • integrating biomolecular interaction networks with high-throughput expression data and other molecular states into...
  • DEseq

  • Referenced in 59 articles [sw10344]
  • mean dependence in count data from high-throughput sequencing assays and test for differential expression...
  • RegulonDB

  • Referenced in 53 articles [sw25948]
  • mapped promoters coming from our own high-throughput mapping efforts. RegulonDB v.6.0 now expands beyond...
  • MCODE

  • Referenced in 49 articles [sw35748]
  • false positives in data from high-throughput interaction techniques. The program is available from...
  • ArrayExpress

  • Referenced in 42 articles [sw29723]
  • Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data...
  • FAMT

  • Referenced in 32 articles [sw11123]
  • multiple testing procedures for high-throughput data as proposed by Friguet...
  • Samtools

  • Referenced in 22 articles [sw14583]
  • suite of programs for interacting with high-throughput sequencing data. It consists of three separate ... HTSlib: A C library for reading/writing high-throughput sequencing data. Samtools and BCFtools both...
  • DESeq2

  • Referenced in 27 articles [sw41938]
  • mean dependence in count data from high-throughput sequencing assays and test for differential expression...
  • VAMPnets

  • Referenced in 19 articles [sw32927]
  • such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transformation...
  • iDNA-Methyl

  • Referenced in 19 articles [sw22423]
  • predictor will become a very useful high-throughput tool for basic research and drug development...
  • Prnam-PC

  • Referenced in 18 articles [sw22422]
  • predictor will become a useful high-throughput tool for identifying methylation sites...
  • CellProfiler

  • Referenced in 17 articles [sw18751]
  • open-source system designed for flexible, high-throughput cell image analysis, CellProfiler. CellProfiler can address...
  • iHSP-PseRAAAC

  • Referenced in 16 articles [sw25193]
  • highly desirable to develop a high-throughput computational tool in this regard. To take...
  • STAR

  • Referenced in 15 articles [sw02515]
  • aligner. Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging...
  • DRAGON

  • Referenced in 14 articles [sw00220]
  • well as for similarity analysis and high-throughput screening of molecule databases. Dragon...
  • GOTM

  • Referenced in 9 articles [sw13869]
  • Gene Ontology hierarchies. Microarray and other high-throughput technologies are producing large sets of interesting ... with other gene sets from other high-throughput analyses. GOTree Machine generates a GOTree...
  • HTSeq

  • Referenced in 8 articles [sw16898]
  • Python framework to work with high-throughput sequencing data. Motivation: A large choice of tools ... standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project...
  • RAST

  • Referenced in 8 articles [sw17158]
  • shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided ... wide range of researchers. Results: A high-throughput pipeline has been constructed to provide high...
  • DEGseq

  • Referenced in 11 articles [sw07998]
  • expressed genes from RNA-seq data. High-throughput RNA sequencing (RNA-seq) is rapidly emerging...