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Showing 3 open source projects for "subread"

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    Subread

    High-performance read alignment, quantification and mutation discovery

    The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction.
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    Downloads: 457 This Week
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  • 2

    hppRNA

    A Snakemake-based handy parameter-free pipeline for RNA-Seq analysis

    ...It starts from fastq files and will produce gene/isoform expression matrix, differentially-expressed-genes, sample clusters as well as detection of SNP and fusion genes by combination of the state-of-the-art software. The first version handles protein-coding genes, lncRNAs and circRNAs and includes six core-workflows such as (1) Tophat - Cufflink - Cuffdiff; (2) Subread - featureCounts - DESeq2; (3) STAR - RSEM - EBSeq; (4) Bowtie - eXpress - edgeR; (5) kallisto - sleuth; (6) HISAT - StringTie - Ballgown. Please cite the following paper when using this package: Dapeng Wang. hppRNA—a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples. Briefings in Bioinformatics, Volume 19, Issue 4, 20 July 2018, Pages 622–626.
    Downloads: 3 This Week
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  • 3
    THIS PROJECT HAS BEEN MOVED TO http://sourceforge.net/projects/subread THIS PROJECT HAS BEEN MOVED TO http://sourceforge.net/projects/subread THIS PROJECT HAS BEEN MOVED TO http://sourceforge.net/projects/subread THIS PROJECT HAS BEEN MOVED TO http://sourceforge.net/projects/subread THIS PROJECT HAS BEEN MOVED TO http://sourceforge.net/projects/subread THIS PROJECT HAS BEEN MOVED TO http://sourceforge.net/projects/subread THIS PROJECT HAS BEEN MOVED TO http://sourceforge.net/projects/subread PLEASE UPDATE YOUR BOOKMARK!
    Downloads: 0 This Week
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