Releases: davemcg/plaeApp
0.91
Updated scEiaD scVI model once more. We simplified pan species gene name alignment by removing "one to many" or "many to one" name alignments. All expressed genes are still retained in the individual species (if not present in the gene name name merged matrix), but we are less aggressive about merging gene names across species as we discovered some edge cases where many genes were getting merged into one and vice versa. This necessitated a new core gene <-> cell count matrix and thus a new scVI model. We also took the opportunity to add a new mouse retina development dataset from Balasubramanian et al. and a new ocular compartment dataset from Gautam et al. We leverage the new(ish) scANVI scVI approach in which we use the community cell type labels to subtly improve the scVI modelling of the cell types.
Updated diff testing model to a pseudoBulk / DESeq2 based approach. Now run on a per-species basis. Added heatmap visualization which uses the DESeq2 pseudobulk differential experession changes. Fixed bug that removed RPC from the Expression Plot view as well as display zero expression studies. Expression Plot view has a new option which flips flops the facet / x axis from Gene to whatever the cell type label is (CellType, CellType_predict, cluster).
0.80
0.51: New diff testing, tweaked scVI model and UMAP projection
Merge pull request #26 from davemcg/diff_change Updates diff testing for new scEiaD
new scEiaD (2020-12-29)
Updated code for new scEiaD
PseudoBulk data table enhancement
Data table for pseudobulk updated with a separate button to fully download the DT::datatable results. The CSV "button" in DT just downloads what is currently being viewed (no more than 100). Added a link to download the pseudo bulk diff testing results separately from the the full sqlite file.
Went public!
Minor things fixed - typos. Removed a well-based celltype/cluster from view in Diff Testing as it's not of high quality/consistency.
Next major release
Improved 508 compliance (color contrast, UI element order, alt text)
Dotplot bug fix
Faster plot and table display
0.36: Merge pull request #18 from davemcg/dev
- Fix bug in exp_plot
- Add modal (pop-up) legend for meta-plot with LOTS of categories
- Data download section added.
- Change log moved to separate section.
- CSS tweaked to show links in blue.
- First overview table updated to improve contrast.
- UMAP plots axis fixed.
0.35
- Moved Overview tables to html for improved rendering and switched over color-blind friendly palette.
- Temporarily removed Temporal Plotting section.
- Improved filtering for Facet Plot.
- DotPlot plotting fixed and improved.
- Back-end server.R code moved into separate functions.
- Colors fixed so they stay consistent when filtering/subsetting the plots.
- Site now starts from scratch in under 5 seconds with improved fst-based data loading and pre-calculating more operations.