Regulatory effect prediction

Prediction of gene expression from chromatin accessibility

Description

Missing ‘task_description’

Summary

viewof color_by_rank = Inputs.toggle({label: "Color by rank"})
viewof scale_column = Inputs.toggle({label: "Rescale per column"})

funkyheatmap(
    funky_heatmap_args.data,
    funky_heatmap_args.columns,
    funky_heatmap_args.column_info,
    funky_heatmap_args.column_groups,
    funky_heatmap_args.palettes,
    funky_heatmap_args.expand,
    funky_heatmap_args.col_annot_offset,
    funky_heatmap_args.add_abc,
    scale_column,
    {
        fontSize: 14,
        rowHeight: 26,
        rootStyle: 'max-width: none',
        colorByRank: color_by_rank
    }
);

Figure 1: Overview of the results per method. This figures shows the mean of the scaled scores (group Overall), the mean scores per dataset (group Dataset) and the mean scores per metric (group Metric).

funkyheatmap = (await require('d3@7').then(d3 => {
  window.d3 = d3;
  return import('https://unpkg.com/funkyheatmap-js@0.1.7');
})).default;

Metrics

• Median Pearson correlation¹: Median Pearson correlation between predicted and true gene expression over all genes.

• Median Spearman correlation¹: Median Spearman correlation between predicted and true gene expression over all genes.

Results

Results table of the scores per method, dataset and metric (after scaling). Use the filters to make a custom subselection of methods and datasets. The “Overall mean” dataset is the mean value across all datasets.

Details

Methods

• BETA²: TODO. Software version 1.0. Links: Docs.

• Random Scores⁴: TODO. Links: Docs.

• True Scores⁴: TODO. Links: Docs.

Baseline methods

• Random Scores: TODO.

• True Scores: TODO.

Datasets

• sciCAR Mouse Kidney with cell clusters³: 11k cells from adult mouse kidney sequenced by sci-CAR, a combinatorial indexing-based co-assay that jointly profiles chromatin accessibility and mRNA.

Download raw data

Task info Method info Metric info Dataset info Results Quality control

Quality control results

Category	Name	Value	Condition	Severity
Scaling	Worst score beta pearson_correlation	-3.329978	worst_score >= -1	✗✗✗
Task info	Pct 'task_description' missing	1.000000	percent_missing([task_info], field)	✗✗

Visualization of raw results