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RSEQREP
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RSEQREP

RSEQREP (RNA-Seq Reports) is a tool for complete RNA-seq analysis. The RSEQREP algorithm runs on an RSEQREP Amazon Virtual Machine Image (AMI) hosted by AWS, or on a local Linux machine (Ubuntu). The RSEQREP has automated, customizable analysis methods for reference alignment, reference alignment quality control, data normalization, data compression, identification of differentially expressed genes, identification of co-expressed gene clusters, enriched pathways, and heatmaps. The algorithm outputs a PDF report, publication-ready tables, and figures.



RSEQREP

RSEQREP (RNA-Seq Reports) is a tool for complete RNA-seq analysis. The RSEQREP algorithm runs on an RSEQREP Amazon Virtual Machine Image (AMI) hosted by AWS, or on a local Linux machine (Ubuntu). The RSEQREP has automated, customizable analysis methods for reference alignment, reference alignment quality control, data normalization, data compression, identification of differentially expressed genes, identification of co-expressed gene clusters, enriched pathways, and heatmaps. The algorithm outputs a PDF report, publication-ready tables, and figures.

Topic

RNA-seq

Details

  • Operation: Enrichment analysis; Expression data visualisation; Expression profile clustering; Pathway or network prediction; Sequencing quality control; Standardisation and normalisation
  • Software interface: Command-line user interface
  • Language: R;Perl
  • Operating system: Linux
  • License: GNU GPL v3, GNU AGPL v3, LaTeX Project Public License v.1.3(c)
    • Cost: Free
  • Version name: 1.1.3
    • Maturity: Stable
  • Credit: The Emmes Corporation, he National Institutes of Allergy and Infectious Disease, part of the National Institutes of Health in the Department of Health and Human Services.
  • Contact: Johannes B. Goll jgoll _at_ emmes.com
  • Collection: -

Publications

Jensen TL, Frasketi M, Conway K, Villarroel L, Hill H, Krampis K, Goll JB "RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting." F1000Res. 2017 Dec 21;6:2162. 2017. https://doi.org/10.12688/f1000research.13049.2
PMID: 30026912
PMCID: PMC6039931


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