Release for JOSS publication

v3.0.1

add link to README

V3 release

• Rewrote the entire application from scratch (expect a few bugs :fingerscrossed:)
• Officially support explore mode to visually explore pre-analyzed datasets
• Gene set enrichment to identify enriched gene sets among the top markers for each cluster
• Markers and gene set panels can be used on any annotation and not just the kana-identified clusters
• Download results as CSV for both markers and gene sets
• Support Perturb-seq and similar CRISPR based modalities
• Gallery orients vertically or horizontally based on browser and available screen widths
• UX improvements, text edits to various components for new functionality

and all the other changes (~180+ commits) from #158

Integration with `ExperimentHub`

You can now choose a supported single-cell dataset from Bioconductor's ExperimentHub

Support for SummarizedExperiment formats

• A SummarizedExperiment object saved in the RDS (*.rds) format. We support any SummarizedExperiment subclass containing a dense or sparse count matrix (identified as any assay with name starting with "counts", or if none exist, just the first assay). For a SingleCellExperiment, any alternative experiment with name starting with "hto", "adt" or "antibody" is assumed to represent CITE-seq data.
• Minor fixes to UI issues when switching between modalities, versus mode and selecting weights

Versus mode

Features:

• Enable versus mode to compare markers across two clusters.
• By default, the general mode will rank markers for a cluster or custom selection based on the comparison to all other clusters or cells.
• Users can instead enable versus mode to compare markers between two clusters or between two custom selections. This is useful for identifying subtle differences between closely related groups of cells.
• PR: (#141)

Perform analysis on a subset of cells

• UI to subset cells based on annotations
• Option to skip QC (RNA and ADT) steps, e.g., when processing filtered datasets. (https://github.com/jkanche/kana/pull/130)
• Updated the analysis loader for new bakana calls.
• Sort custom selection indices (#131)
• more error catching
• update docs, changelog, bump version

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Support for a multi-modal analysis of ADT + RNA

Features

• Added new parameter elements for ADT, integrated analysis.
• Support multiple modalities in the marker selection.
• Support multiple modalities in diagnostic plots.
• Use latest multi-modal-aware version of bakana.
• Added a logo to the repo for safety.
• PR: (https://github.com/jkanche/kana/pull/125)

Linked embeddings & persistent selections

Features

• PR (#104)
• Visually compare embeddings across annotations
• With linked embeddings, you can now make lasso selections on any plot and the app automatically highlights these cells across all visualizations
• Save and restore state of the embedding from the gallery
• Export plots from the interface as png
• Drag and drop, and reorganize the gallery in any order you like

Bug Fixes:

• Reindexing when switching between embeddings (#103)
• DimPlots registering callbacks too many times
• Many UI enhancements/css issues