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

    3786 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

    3428 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

    3324 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

    2918 days ago

  • Scallop: reference-based transcriptome assembler for RNA-seq

    Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be proved preserving all phasing paths from reads and p...

    Tags: Scallop, reference-based, transcriptome, assembler, RNA-seq, Tools

    2142 days ago

  • Installing Trinity !

    Download this https://github.com/trinityrnaseq/trinityrnaseq/releases/tag/Trinity-v2.6.6 ➜ cd trinityrnaseq-Trinity-v2.6.6 ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ make Using gnu compiler for Inchworm and Chrysalis cd Inchworm && (test -e configure || autoreconf) \ ...

    Tags: Installing, Trinity, RNA-seq, NGS, Assembly, Transcriptomics

    2086 days ago

  • RNA-seq Analysis Workshop Course Materials

    RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experiment is performed. It allows reads to be aligned against the reference genome and significantly improves our ability to reconstruct transcripts. This cate...

    Tags: RNA-seq, Analysis, Workshop, Course, Materials, NGS

    2086 days ago

  • NCBI Magic-BLAST

    Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up ...

    Tags: NCBI, Magic-BLAST, Documentation, RNA-seq, Mapping, BLAST

    2043 days ago

  • BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks

    With BioJupies you can produce in seconds a customized, reusable, and interactive report from your own raw or processed RNA-seq data through a simple user interface BioJupies now supports user accounts! Sign in from the top right corner of the page for access to unlimited private notebooks, RNA-...

    Tags: BioJupies, Automatically, Generates, RNA-seq, Data, Analysis, Notebooks

    1184 days ago

  • Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

    Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software ...

    Tags: Rcorrector, efficient, accurate, error, correction, Illumina, RNA-seq, reads

    1504 days ago