TooManyCellsInteractive: A visualization tool for dynamic exploration of single-cell data
Bibliographic record
Abstract
BACKGROUND: As single-cell sequencing technologies continue to advance, the growing volume and complexity of the ensuing data present new analytical challenges. Large cellular populations from single-cell atlases are more difficult to visualize and require extensive processing to identify biologically relevant subpopulations. Managing these workflows is also laborious for technical users and unintuitive for nontechnical users. RESULTS: We present TooManyCellsInteractive (TMCI), a browser-based JavaScript application for interactive exploration of cell populations. TMCI provides an intuitive interface to visualize and manipulate a radial tree representation of hierarchical cell subpopulations and allows users to easily overlay, filter, and compare biological features at multiple resolutions. Here we describe the software architecture and demonstrate how we used TMCI in a pan-cancer analysis to identify unique survival pathways among drug-tolerant persister cells. CONCLUSIONS: TMCI will facilitate exploration and visualization of large-scale sequencing data in a user-friendly way. TMCI is freely available at https://github.com/schwartzlab-methods/too-many-cells-interactive. An example tree from data within this article is available at https://tmci.schwartzlab.ca/.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".