BGPT: Create Graphs: Reproduce Fan 2015 figures from raw data

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Fan 2015 Figure Reproduction — Raw-Data Requirement

What I can and can’t do right now

I cannot accurately “reproduce Fan 2015 figures from raw data” because the raw underlying data files (or the exact raw-data source tables) were not provided in your message.
I also don’t have enough metadata to know which Fan (2015) paper, which figure panels, and which raw datasets map to each panel.
Because you requested “no hypothetical/simulated data” and “no statements without citations,” any attempt to redraw would risk being incorrect or non-reproducible.

Upload what I need (fastest path)

The full citation for “Fan 2015” (authors + title, or DOI).
Which figure(s) you want reproduced (e.g., “Figure 2A–2D”, “Figure S3” etc.).
Raw data needed to regenerate each panel (commonly: CSV/TSV tables, count matrices, alignment-derived tables, experiment metadata spreadsheets, or supplementary “source data” files).
If Fan 2015 provides a processing pipeline, also upload any supplementary methods scripts or parameter files.

Once you upload the raw files (or paste the exact raw tables), I will generate Plotly graphs panel-by-panel and validate that the axes, binning, normalization, and statistical annotations match the paper.

Reproducibility checklist (what I will verify once raw data is provided)

Axis transforms (e.g., log10 vs log2, offsets, scaling to % or per-sample).
Normalization (per-cell/per-sample, library-size, control normalization, batch correction assumptions—only if present in raw-data documentation).
Binning/aggregation (bin edges, smoothing kernels, replicate handling).
Statistical overlays (error bars: SD vs SEM; CI computation; tests used and how p-values are computed).
Labeling (legend order, units, cohort/group naming, color mapping).

A ready-to-run Science Agent (iterative raw-data graphing)

Upload the raw files (and/or paste links) before running, so the agent can iteratively locate the correct columns, compute the plotted quantities from the raw tables, and render the Plotly panels.