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It also allows for exploratory analysis when no replicates are available.\n\nThe app also provides svaseq **Surrogate Variable Analysis** for **hidden batch** effect detection. The user can then include Surrogate Variables (SVs) as adjustment factors for downstream analysis (eg. differential expression). For more information on svaseq, go to\u003ca href=\"https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#using-sva-with-deseq2\" target=\"_blank\"\u003e this link\u003c/a\u003e\n\n### Online/Demo:\nYou can try it online at http://nasqar.abudhabi.nyu.edu/deseq2shiny\n\n### Pre-print:\n[NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization](https://doi.org/10.1101/709980)\n\n### Features\n---\nVarious **visualizations** and **output data** are included:\n\n*   **Clustering**\n\n    *   **R-Log**, **Variance Stabilizing Transformation** (VST) output matrices\n    *   **PCA plots**, **Heatmaps**\n\n*   **Differential Expression**\n\n    *   Comparison Data (**logFC, p-value, etc, sample vs sample**, etc …)\n    *   MA plots\n\n*   **Gene Expression**\n\n    *   Gene **Boxplots**\n      \n      \n---\n![alt text](screenshotdeseq2.png \"Input Data\")\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnasqar%2Fdeseq2shiny","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnasqar%2Fdeseq2shiny","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnasqar%2Fdeseq2shiny/lists"}