v3.0.2

• Bugfix: Removed the loe dependency. This dependency was causing issues as it is no longer available in CRAN - however, the dependency itself is no longer used in the package.

v3.0.1

• Bugfix - newest Matrix package (1.5-3) resulted in an issue where cell labels were being dropped, causing issues later in the pipeline. Bug fixed in this release

v3.0.0

This release includes the PhyloVision module, allowing users to use concepts from the original VISION pipeline to identify signatures that are autocorrelated on phylogenies, such as those generated with CRISPR/Cas9-based lineage tracers or from B-cell receptor (BCR) sequencing.

This release also supports the analysis of expression data with Hotspot. This analysis framework identifies modules of genes are autocorrelated with one another with respect to some cell-cell similarity metric (e.g. a phylogeny or some low-dimensional embedding).

While most functionality from version < 3.0.0 is preserved, we have deprecated the Trajectory and PC Annotator pipelines. If this is important to your work, you can use VISION version 2.1.0 which is still stable.

To get you started with the new functionality, we have new vignettes on our main documentation website.

v2.1.0

Added parameter sig_gene_threshold with changed default behavior

• Before it was a guideline to filter lowly expressed genes before running VISION
• Now, by default, genes expressed in fewer than 0.1% of cells will be filtered automatically

Bug Fixes:

• Better colors in output when more than 10 categories
• Errors with certain output object accessors
• Selections not saving when loading results server
• Crashes when running on more than 1200 signatures

v2.0.0

Lots of changes for this version.

However the object structure has been refactored. This means that any old saved RDS objects will not work with the viewResults function once the code has been upgraded. To resolve this, either re-create the objects or use the latest v1.x release of VISION. Incompatible changes like this will be avoided in the future, but in this case a refactor was long needed.

• Added support for surface protein data (e.g., CITE-seq)
  • This data is entered separately using the proteinData argument
  • Autocorrelation scores will be computed on protein data
  • Differential expression tests will also test protein data
  • Can view protein vs. protein (FACS-style) in output report
• Improved handling of sparse data
  • When inputing sparse expression data, the processing pipeline will no longer expand this data to dense at any stage
• Additional improvements for performance and memory usage
• New exported pipeline functions for custom workflows
• UI Improvements
  • Can see multiple, different views simultaneously in the output (by unchecking the 'Update All?' changes only affect the selected plot
  • Y-axis for feature histograms can be log-scaled
  • Filtering (FDR) and Export for DE results table
  • Caching of DE results to avoid re-running
  • Additional DE options (subsampling, gene filtering) for reduced run times
  • Improved signature-gene heatmap

Many thanks to @Yanay1 for improvements to the DE results and heatmap!

v1.1.1

• Added support for Seurat 3.X objects
• Removed gzmem as a suggested dependency
• Various style fixes
• Bugfixes
  • Fixed issue with selection on high-dpi displays
  • Better Encoding of URI Components

v1.1.0a

New release for Zenodo DOI webhook

v1.1.0

• Added differential expression testing to the output report
  • Thanks to @Yanay1 (Yanay Rosen)
• Added gene-signature importance calculation
• More flexible projection plotting
• Added UMAP as a projection method

v1.0.1

• Bugfixes related to caching in the output report
• Change default cellsPerPartition value to 10
• Change default filterThreshold parameter value to 5% in applyMicroClustering (for consistency with Vision constructor)

v1.0.0

• Added Layout Options to the output report
• Selected cells can now be saved/loaded
• Addition of "get*"-style accessor methods to the VISION object
• Added an interface to Seurat objects
• Added convenience methods for working with outputs from 10x Genomic's CellRanger
• Note: Some changes were made to the Vision object structure and how results are stored. If updating to 1.0.0, older Vision objects may need to be re-created and re-run before using viewResults