• BABAR

  • Referenced in 1 article [sw18997]
  • transcriptomic data to be readily compared and re-analysed in the light of new data ... Excellent software exists for the normalisation and analysis of microarray data but many data have ... with the microarray data in excellent agreement with RT-PCR analysis. When applied ... differentially expressed genes or network inference analysis from transcriptomic datasets...
  • ParaKMeans

  • Referenced in 4 articles [sw29731]
  • transcriptome of many biological systems has generated an enormous amount of data. A common technique ... organize and analyze microarray data is to perform cluster analysis. While many clustering algorithms have...
  • MAST

  • Referenced in 6 articles [sw30709]
  • single-cell RNA sequencing data. Single-cell transcriptomics reveals gene expression heterogeneity but suffers from ... part, generalized linear model for such bimodal data that parameterizes both of these features ... variation. Our model provides gene set enrichment analysis tailored to single-cell data. It provides...
  • pcaReduce

  • Referenced in 1 article [sw23916]
  • transcriptomics data at the single cell level. A frequent requirement of single cell expression analysis...
  • CLIPZ

  • Referenced in 3 articles [sw29589]
  • CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins ... immunoprecipitation (CLIP) coupled with deep sequencing provides transcriptome-wide coverage as well as high resolution ... partly due to their vast volume, the data that were so far generated in CLIP ... have developed the CLIPZ database and analysis environment. Binding site data for RBPs such...
  • Sincera

  • Referenced in 2 articles [sw23915]
  • While recent studies using single cell transcriptome analysis illustrate the power to measure and understand ... systems, processing large amounts of RNA-seq data from heterogeneous cell populations creates the need...
  • ASTALAVISTA

  • Referenced in 3 articles [sw17177]
  • ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets ... ASTALAVISTA can characterize AS for whole transcriptome data from reference annotations (GENCODE, REFSEQ, ENSEMBL...
  • nsiGGM

  • Referenced in 1 article [sw22173]
  • model is inevitably dependent on post hoc analysis in order to confirm biological significance ... attempt not only to combine transcriptomic data but also to embed pathway information, well-ascertained...
  • SeqBuster

  • Referenced in 1 article [sw29583]
  • bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications ... sequencing data requires bioinformatic tools offering a wide perspective of the small RNA transcriptome. Here ... analysis for mapping purposes and in the different analysis modules for data manipulation. To overcome...
  • PALMapper

  • Referenced in 1 article [sw31862]
  • sequences produced by RNA-Seq enhance transcriptome analysis and promise great opportunities for the discovery ... alternative transcripts. One way to analyze this data is aligning the reads against a reference...
  • Oases

  • Referenced in 3 articles [sw17027]
  • Motivation: High-throughput sequencing has made the analysis of new model organisms more affordable. Although ... data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome...
  • ASPicDB

  • Referenced in 2 articles [sw17172]
  • mechanism responsible for the expansion of transcriptome and proteome complexity in human and other organisms ... several online resources devoted to alternative splicing analysis are available they may suffer from limitations ... prevent the full exploitation of the available data. Furthermore, current resources provide limited query...
  • Radio-iBAG

  • Referenced in 1 article [sw32135]
  • introduce the use of sparse Principal Component Analysis (sPCA) to extract a sparse ... Cancer Genome Atlas glioblastoma multiforme data set, where-in we integrate magnetic resonance imaging-based ... biomarkers along with genomic, epigenomic and transcriptomic data. Our model identifies important magnetic resonance imaging...
  • stringgaussnet

  • Referenced in 0 articles [sw15372]
  • Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor. A toolbox ... WGCNA’ approach, from DE genes analysis results and expression data. Additional functions are provided...
  • Yanagi

  • Referenced in 1 article [sw33123]
  • quantification. Analysis of differential alternative splicing from RNA-seq data is complicated by the fact ... transcriptome into disjoint regions to create a segments library from a complete transcriptome annotation that ... transcriptome. In this paper, we formalize this concept of transcriptome segmentation and propose an efficient ... characterize the segment libraries for the reference transcriptomes of Drosophila melanogaster and Homo sapiens. Finally...
  • SpliceTrap

  • Referenced in 3 articles [sw29591]
  • every exon is crucial for generating accurate transcriptomic maps and studying the regulation ... inclusion levels using paired-end RNA-seq data. Unlike other tools, which focus on full ... SpliceTrap both by simulation and real data analysis, and compared it to state...
  • GENE-counter

  • Referenced in 1 article [sw20039]
  • computational pipeline for the analysis of RNA-Seq data for gene expression differences. GENE-counter ... data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic ... compliant program of preference. To analyze data for differential gene expression, GENE-counter ... counter to process the data. Collectively, the support from analysis of microarrays as well...
  • METRADE

  • Referenced in 1 article [sw28181]
  • term multi-omic (transcriptomic and metabolic) evolution, thus enabling comparative analysis of metabolic conditions ... than in the original space of microarray data. We finally validate our methods...
  • FX

  • Referenced in 1 article [sw12023]
  • short RNA-Seq reads, FX uses a transcriptome-based reference primarily, generated from ... human genome reference. FX allows analysis of RNA-Seq data on cloud computing infrastructures, supporting...
  • e2eXpress

  • Referenced in 1 article [sw35772]
  • Microarrays. e2eXpress incorporates basic data management and analysis tasks with novel approaches for mining various ... required to mine the transcriptome in conjunction with extraneous data sources that can lead...