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  • mixOmics
  • Referenced in 29 articles [sw09508]
  • throughput technologies, such as omics data (e.g. transcriptomics, metabolomics or proteomics data) that require...

  • TopHat
  • Referenced in 23 articles [sw17157]
  • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. TopHat...

  • RSEM
  • Referenced in 12 articles [sw17160]
  • particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes ... Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification ... particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable...

  • iRNA-3typeA
  • Referenced in 17 articles [sw27660]
  • sequences from Homo sapiens and Mus musculus transcriptomes that the success rates achieved...

  • STAR
  • Referenced in 14 articles [sw02515]
  • align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced...

  • SC3
  • Referenced in 8 articles [sw23914]
  • characterization of cell types based on global transcriptome profiles. We present single-cell consensus clustering ... capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients...

  • DEGseq
  • Referenced in 11 articles [sw07998]
  • rapidly emerging as a major quantitative transcriptome profiling platform. Here, we present DEGseq...

  • Oncomine
  • Referenced in 7 articles [sw17289]
  • microarrays have been widely applied to cancer transcriptome analysis; however, the majority of such data ... collecting, standardizing, analyzing, and delivering cancer transcriptome data to the biomedical research community. Our analysis...

  • curatedOvarianData
  • Referenced in 6 articles [sw17291]
  • clinically annotated data for the ovarian cancer transcriptome. This article introduces a manually curated data ... clinically oriented investigation of the ovarian cancer transcriptome. The package and pipeline for producing...

  • MultiCluster
  • Referenced in 6 articles [sw30715]
  • struggle to fully extract the insights into transcriptome complexity contained in the data. We propose ... tensor decomposition which permits the investigation of transcriptome variation across individuals and tissues simultaneously...

  • SNN-Cliq
  • Referenced in 6 articles [sw34296]
  • Identification of cell types from single-cell transcriptomes using a novel clustering method. Results ... neighbor (SNN)-Cliq that clusters single-cell transcriptomes. SNN-Cliq utilizes the concept of shared...

  • MAST
  • Referenced in 8 articles [sw30709]
  • single-cell RNA sequencing data. Single-cell transcriptomics reveals gene expression heterogeneity but suffers from...

  • GeneCards
  • Referenced in 8 articles [sw30714]
  • data from  150 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information...

  • Salmon
  • Referenced in 7 articles [sw31865]
  • unsorted BAM file with alignments to the transcriptome produced with your favorite aligner...

  • SIMoNe
  • Referenced in 6 articles [sw06067]
  • from either steady-state or time-course transcriptomic data. Note that with both type...

  • BioNet
  • Referenced in 5 articles [sw13828]
  • includes the statistics for the integration of transcriptomic and functional data with biological networks...

  • BEETL
  • Referenced in 5 articles [sw23284]
  • this technique, we show that BWTs of transcriptomic and genomic reads can be compared...

  • AceView
  • Referenced in 3 articles [sw23000]
  • evidences the beauty and complexity of mammals’ transcriptome, and the relative simplicity of the nematode ... plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding...

  • Gene Resource Locator
  • Referenced in 3 articles [sw37100]
  • Gene Resource Locator: gene locus maps for transcriptome analysis. Since the advent of the draft ... sequence there has been growing interest in transcriptome analysis based on genomic data. The Gene...

  • gNCA
  • Referenced in 4 articles [sw08821]
  • determining transcription factor activity based on transcriptome: identifiability and numerical implementation. Network Component Analysis...