Results for "rna-seq"

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  • Modular, efficient and constant-memory single-cell RNA-seq preprocessing

    With kallisto | bustools you can Generate a cell x gene or cell x transcript equivalence class count matrix Perform RNA velocity and single-nuclei RNA-seq analsis Quantify data from numerous technologies such as 10x, inDrops, and Dropseq. Customize workflows fo...

    Tags: Modular, efficient, constant, memory, single-cell, RNA-seq, preprocessing, bustool, kallisto

    1088 days ago

  • LncPipe:A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets

    The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed lncRNAs annotation strategy, optimized calculating eff...

    Tags: LncPipe, Nextflow, pipeline, comprehensive, analyses, long, non-coding, RNAs, RNA-seq, datasets

    923 days ago

  • RNA-seq workflow: gene-level exploratory analysis and differential expression

    Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count datasets for downstream analysis. We will perform explo...

    Tags: RNA-seq, workflow, gene-level, exploratory, analysis, differential, expression

    901 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

    3668 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

    3625 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

    3598 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

    3458 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

    3428 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

    3394 days ago

  • Rosalind Bioinformatics problems !!!

    Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works. http://rosalind.info/problems/list-view/

    Tags: Bioinformatics, Computational Biology, NGS, Genome, RNA-Seq, Algorithms, Online, Rosalind

    3388 days ago