Visualization Community | St. Jude Cloud

GenomePaint MA+Volcano plots Example

Zhou Lab

Sep 28, 2021

RNA Sequencing

Use the interactive MA and Volcano plot for exploring differentially expressed genes. Hover over the data points to view calculated values per gene. Hovering also reveals the location of the gene in both plots. Clicking on the data point opens the genome browser to view any available RNAseq coverage data. Learn more about the MA+Volcano plots.

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runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  genome: "hg19",
  noheader: 1,
  mavolcanoplot: {
    url: "https://pecan.stjude.cloud/static/pp-support/example.files/DIPG_H33K27MvsWT_noACVR_adj.txt",
    tracks: [
      {
        "name": "Demo RNA-seq coverage",
        "strand1": {
          "file": "proteinpaint_demo/hg19/mavb/mavb_demo_sense.bw"
        },
        "strand2": {
          "file": "proteinpaint_demo/hg19/mavb/mavb_demo_antisense.bw",
          "normalize": {
            "dividefactor": -1
          }
        },
        "type": "bigwigstranded"
      }
    ]
  }
});

Visualization Code

runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  genome: "hg19",
  noheader: 1,
  mavolcanoplot: {
    url: "https://pecan.stjude.cloud/static/pp-support/example.files/DIPG_H33K27MvsWT_noACVR_adj.txt",
    tracks: [
      {
        "name": "Demo RNA-seq coverage",
        "strand1": {
          "file": "proteinpaint_demo/hg19/mavb/mavb_demo_sense.bw"
        },
        "strand2": {
          "file": "proteinpaint_demo/hg19/mavb/mavb_demo_antisense.bw",
          "normalize": {
            "dividefactor": -1
          }
        },
        "type": "bigwigstranded"
      }
    ]
  }
});

GenomePaint MA+Volcano plots Example

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Visualization Code