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  • DEseq
  • Referenced in 60 articles [sw10344]
  • mean dependence in count data from high-throughput sequencing assays and test for differential expression...

  • 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...

  • 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...

  • CNV-seq
  • Referenced in 11 articles [sw17970]
  • detect copy number variation using high-throughput sequencing. Background: DNA copy number variation...

  • RAST
  • Referenced in 8 articles [sw17158]
  • metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing ... researchers. Results: A high-throughput pipeline has been constructed to provide high-performance computing ... pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein...

  • ShortRead
  • Referenced in 6 articles [sw16605]
  • input, quality assessment and exploration of high-throughput sequence data. ShortRead is a package ... quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided...

  • F-Seq
  • Referenced in 5 articles [sw17297]
  • density estimator for high-throughput sequence tags. Summary: Tag sequencing using high-throughput sequencing technologies...

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

  • TopKLists
  • Referenced in 6 articles [sw13900]
  • visualization of multiple omics ranked lists. High-throughput sequencing techniques are increasingly affordable and produce ... massive amounts of data. Together with other high-throughput technologies, such as microarrays, there...

  • SeqMap
  • Referenced in 6 articles [sw17145]
  • places in a reference genome where each sequence may come from. This task is essential ... analysis of data from ultra high-throughput sequencing machines. With a carefully designed index-filtering...

  • MultiCluster
  • Referenced in 6 articles [sw30715]
  • nonnegative tensor decomposition. The advent of high-throughput sequencing technologies has led to an increasing...

  • BEAGLE

  • Referenced in 6 articles [sw12586]
  • evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands...

  • HiTEC
  • Referenced in 3 articles [sw13916]
  • HiTEC: accurate error correction in high-throughput sequencing data. Motivation: High-throughput sequencing technologies produce ... very large amounts of data and sequencing errors constitute one of the major problems ... method to correct reads produced by high-throughput sequencing methods. Our approach provides significantly higher...

  • GRASS
  • Referenced in 5 articles [sw12609]
  • increasing availability of second-generation high-throughput sequencing (HTS) technologies has sparked a growing interest...

  • ANNOVAR
  • Referenced in 4 articles [sw17295]
  • from high-through put sequencing data. High-throughput sequencing platforms are generating massive amounts...

  • GutenTag
  • Referenced in 5 articles [sw35329]
  • GutenTag: High-Throughput Sequence Tagging via an Empirically Derived Fragmentation Model. Shotgun proteomics...

  • Bismark
  • Referenced in 5 articles [sw23504]
  • bisulfite treatment of DNA and high-throughput sequencing (BS-Seq) can capture a snapshot...

  • ScaffMatch
  • Referenced in 5 articles [sw23973]
  • maximum weight matching. MOTIVATION: Next-generation high-throughput sequencing has become a state...

  • Minfi
  • Referenced in 6 articles [sw23478]
  • genomic features. Although less comprehensive than high-throughput sequencing-based techniques, this product is more ... most widely used DNAm high-throughput measurement technology over the next several years. RESULTS: Here ... previously thought to be possible only with sequencing-based methods. AVAILABILITY AND IMPLEMENTATION: http://bioconductor.org...