Visualizations
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GenomePaint BigWig Example
View quantitative data at genomic positions with the BigWig track. Learn more about the BigWig track.
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GenomePaint BAM Track Example (beta)
View sequence alignment data from BAM files. Features include: viewing soft clips, on-the-fly checks for mismatches, switching between single and paired mode, etc. The unique features specific to ProteinPaint include: A “global” view of almost all the reads i...
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GenomePaint VCF Track Example
The VCF track features a population frequency filter, coverage-VAF plot, sample line plot, boxplot by genotype, and sophisticated methods for displaying metadata (see summary here). The current implement only accepts SNV/indel data. Learn more about the VCF tr...
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GenomePaint Allele-specific expression (ASE) Example - beta
The allele-specific expression (ASE) track annotates the tumor gene expression. Scroll through the color coded FPKM values on the right to reveal the ASE status: mono-allelic, bi-allelic, uncertain, or no information available. Clicking on the DNA markers repr...
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GenomePaint Allelic imbalance Example
St. Jude's own Dr.Xiaotu Ma coined the term "AI Check" after designing this visualization. Compare the allelic imbalance of heterozygous SNP markers in a tumor genome against a patient's germline genome, as a targeted method for evaluating loss-of-he...
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GenomePaint Profile Gene Value Example
The profile gene value (PVG) track is a combination of genomic profiling results and gene-level numerical values over a set of sample. Hover over the bars to reveal more information about the chromatin states. Pair with the chromatin data other types of gene v...
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ProteinPaint Expression Rank Example
The expression rank track shows the ranking of gene expression in each sample, amongst all samples from the same cancer group. Expression rankings are rendered as bar plots under the 0 to 100 scale, 0 for lowest among the group, 100 for highest. Hover over a b...
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GenomePaint Hi-C Example
Visualize Juicebox .hic files from Hi-C experiments. The Hi-C track also supports a whole genome view, example here. Learn more about the Hi-C track.
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GenomePaint JSON BED Example
View genomic feature annotation with the JSON BED track. Hover over an area of interest to see the characterization of that genomic feature. Learn more about the JSON BED track.
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