From: Rapid single cell evaluation of human disease and disorder targets using REVEAL: SingleCell™
HCA whitepaper requirements | Functionality | Functionality in Reveal: SingleCell |
---|---|---|
At least one developer-oriented portal providing a platform (e.g. FireCloud or Toil) in which developers can bring containerized environments to perform analyses on the data | R & Python API allow users to work in R studio or Python and directly select data from REVEAL: SingleCell | |
At least one user-oriented portal providing interactive interfaces to the data; for example: | R & Python API | |
Quantifying the expression of a given gene (e.g., marker genes specified by user) across cell types, shown in several popular modalities (e.g., low-d plots, heatmaps, violin plots) | SingleCellviewer and Plotly connecting to REVEAL: Singlecell R & Python API | |
Showing clustering of individual cells from an experiment based on expression profiles; | R & Python API clustering routines | |
Painting cell clusters (ordinations) by metadata (technical and experimental) to identify batch effects and visualize biological groupings (depending on the type of metadata); | SingleCellviewer and Plotly connecting to REVEAL: Singlecell R & Python API | |
Visualizing gene signatures by several modalities, including heatmaps and dot plots of average expression by cell group; and | SingleCellviewer and Plotly connecting to REVEAL: Singlecell R & Python API | |
Cross-correlating gene expression with epigenetic markers. | Using the REVEAL: SingleCell R & Python API | |
Multiple query-oriented portals with APIs targeting custom access patterns, for example: Tag based queries | ||
Querying all gene expression tables generated with a particular analysis | Using the REVEAL: SingleCell Rest API & R notebook | |
Querying all cells for those that match the expression pattern of a target cell and return the metadata for the matching cells | Using the REVEAL: SingleCell Rest API & R notebook | |
Querying all raw data for a specific tissue type, ranked based on a custom combination of quality-control metrics. | Using the REVEAL: SingleCell Rest API & R notebook | |
Housekeeping requirements | ||
Loading data | Using the REVEAL: SingleCell Rest API & R notebook | |
Adding tags after data load | Using the REVEAL: SingleCell Rest API & R notebook | |
Deleting data | Using the REVEAL: SingleCell Rest API & R notebook |