[Clare72]

VFB's scRNAseq data is moving from the FlyBase/SCEA loads (FBlc ids) to VFB's own curation in vfb-scRNAseq (17 datasets, VFBseq ids). The data release with the 17 VFBseq datasets is live.

• Data/scRNAseq/_index.md:

  • The provenance paragraph is rewritten: VFB curates the datasets itself, maps the authors' clusters to FBbt as composed primarily of, and doesn't show held clusters.
  • The datasets table now lists the 17 VFBseq datasets, linked to their reports, with stage, clusters (2,186 in total), genes and study.

• Data/stages.md:

  • The 24 FBlc rows become 17 VFBseq rows, each under its earliest stage.
  • The stage counts and the pupa text are updated.

• Tutorials/Website/scRNAseq.md: Data sources and processing is rewritten for the new pipeline:

  • curation, using control samples where a study compares treatments;
  • FBbt mapping, with held clusters;
  • CPM, the extent > 0.2 filter and current FlyBase gene ids.

• New: Samples, Assays and Clusterings (scRNAseq: term info and queries for Samples, Assays and Clusterings; stage and tissue columns; strain stocks VFBquery#136). The Queries Reference covers the 9 new queries, the stage and tissue columns (a cluster's own stage against its Samples' stages, and how those collapse), Cells/Genes, and Find fly stocks for strains. The scRNAseq data page and tutorial point to them and use the query's current name, "scRNAseq data for…".

Built locally with Hugo 0.168.0 (production uses 0.122.0). All three pages render, with 17 VFBseq links and no FBlc references.

Before merging: check that a few of the dataset links (e.g. VFBseq_00001758, VFBseq_00003265) open on the live site. Also needs VFBquery#136 deployed.

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