Results for "rna-seq"

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  • RNA-Seq Data Pathway and Gene-set Analysis Workflows

    It describe the GAGE (Luo et al., 2009) /Pahview (Luo and Brouwer, 2013) workflows on RNA-Seq data pathway analysis and gene-set analysis. The gage package (2.12.0) now includes a new tutorial, “RNA-Seq Data Pathway and Gene-set Analysis Workflows“. First cover a full workf...

    Tags: R, Bioconductor, RNA-seq, GAGE, Pathway

    1498 days ago

  • Surrogate Variable Analysis (SVA)

    The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constr...

    Tags: RNA-seq, Genomics, R, Bioconductor

    1140 days ago

  • Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer'

    Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer' Abstract Whole exome DNA sequencing (WES) or whole genome DNA sequencing (WGS) allows detection of mutations and polymorphisms in all exonic and genomic regions, respectively, while messenger RNA sequencin...

    Tags: NGS, data analysis, genomics, transcriptomics, DNA-seq, RNA-seq

    1036 days ago

  • RNA-Seq De novo Assembly Using Trinity

    Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied seq...

    Tags: Bioinformatics, NGS, RNA-seq, Assembly, Trinity, Illumina

    630 days ago

  • Encode sequencing data freely available to download and use for academic means

    In Encode, regulatory elements investigated via DNA hypersensitivity assays, assays of DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins that interact with DNA, including modified histones and transcription factors, followed by sequencing (ChIP-Seq). More information: h...

    Tags: Encode, UCSC, genome browser, Sequencing, RNA-Seq, Chip-Seq, Epigenomics, Methylation, histone modification, regulatory elements, HMM

    1371 days ago

  • New RNA Seq tool

    "By removing the time-consuming step of read mapping, the authors reported, Sailfish able to provide quantification estimates 20–30 times faster than current methods without loss of accuracy." Tool link: http://www.cs.cmu.edu/~ckingsf/software/sailfish/

    Tags: Sequencing, RNA-Seq

    1328 days ago

  • GenXPro GmbH

    GenXPro GMbH is service provider for entire spectrum of nucleotide-based information of any biological sample. By combining intelligent data reduction techniques and latest next generation sequencing technologies, our service portfolio provides most accurate and cost efficient solu...

    Tags: Sequencing, DNA-Seq, RNA-Seq, MACE, Epigenetics, microRNA, Chip-Seq, RAD-Seq, Methylation-Seq, transcriptomics, GBS, Gene expression, de-novo assembly, breeding, Exome Seq, Rare variants

    1301 days ago

  • Pathway Analysis

    Pathway Analysis is usually performed with aim to enrich the genes with their functional information and reveal the underlying biological mechanisms pursue by genes. Pathway Analysis is not only limited to what biological pathways a particular set of expressed genes follow but also to disclose th...

    Tags: pathway enrichment, kegg, reactome, go, blast2go, RNA-Seq, RNA, Sequencing

    1161 days ago

  • deepTools

    deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, de...

    Tags: Bioinformatics, Computational Biology, NGS, deepTools, Genome, RNA-Seq, Visualization, Tools

    1131 days ago

  • A 3D Map of the Human Genome

    Suhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist. Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Ro...

    Tags: Bioinformatics, Computational Biology, NGS, Genome, RNA-Seq, Visualization, Chromosome, Chromatin

    1096 days ago