Atlas
Gene accessibility
Gene summary
The table below summarizes accessibility scores for selected gene in cells belonging to the same annotation group (cell type, broad cell type, or sample).
For each group, ncells is te total number of cells, ncells_access is the number of cells and percent_acess is the fraction of cells in which a gene is acessible.
A gene is considered acessible if its score is above the selected threshold.
Atlas
Gene accessibility
Gene summary
The table below summarizes accessibility scores for selected gene in cells belonging to the same annotation group (cell type, broad cell type, or sample).
For each group, ncells is te total number of cells, ncells_access is the number of cells and percent_acess is the fraction of cells in which a gene is acessible.
A gene is considered acessible if its score is above the selected threshold.
Atlas
Gene accessibility
Gene summary
The table below summarizes accessibility scores for selected gene in cells belonging to the same annotation group (cell type, broad cell type, or sample).
For each group, ncells is te total number of cells, ncells_access is the number of cells and percent_acess is the fraction of cells in which a gene is acessible.
A gene is considered acessible if its score is above the selected threshold.
1. Annotation selection
Find genes that are specifically acessible in a group of cells.
First select level of clustering (Clusters or Annotation), then select one or more groups of cells for which the gee acessibility will be calculated.
2. Fold change (FC) selection
Select minimum FC threshold to be used for filtering genes. Genes that have FC above this value in all selected groups (if using absolute method) or median FC above this value in all selected groups (if using median method) will be shown in the summary table.
It is also possible to set a maximum FC threshold for non-selected (background) groups of cells. In this case, the summary will only include genes that have FC above minimum threshold in selected groups of cells, and below maximum threshold in all other groups.
3. Generate summary
Click to generate summary using specified parameters.
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Gene table
Acessibility sum is the total summed acessibility of a gene in selected groups of cells (of note, it will be correlated with the number of cells in selected groups).
Acessibility fraction is the percentage of summed acessibility for a gene that come from the selected groups of cells.
Median FC is the median enrichment of acessibility for a gene in selected groups of cells.
Download gene table