v0.2.2

Changes as of Elizabeth's transition

v0.2.1

What's Changed

• Fix some spatial plotting and importing instability; update notebooks and docstrings by @easlinger in #10
• 2.0.1 by @easlinger in #11

New Contributors

• @easlinger made their first contribution in #10

Full Changelog: v0.1.0...v0.2.1

v0.2.0

update config files for v0.2.0 release

v0.1.0

Features

The main class is Omics, from which Spatial and CRISPR inherit methods. The following is a (non-comprehensive) summary of currently-supported major features.

Importing

• From object (scanpy.AnnData, muon.MuData, spatialdata.SpatialData and spatial data updated from AnnData object)
• From CellRanger directory (scRNA-seq, Xenium, Visium)
• From multiple directories (multi-sample)

General

• Harmony Integration
• Preprocessing
• Clustering (Leiden & Louvain)
• Annotation (CellTypist)
• Plotting (dot, heat, matrix, violin, categorically or continuously color-coded UMAP, QC, group comparisons)
• Ligand-Receptor Analysis
• GSEA for Single-Cell & Pseudo-Bulk (some issues, though)
• Causal Network Analysis (some issues, though)

Perturbations & Other Conditions

• Augur
• Mixscape
• Distance Metrics
• Cell Type Composition Analysis

Spatial

• Centrality Metrics
• Cell Type Co-Occurrence
• Neighborhood Enrichment Analysis
• Spatially Variable Genes

Key Outstanding Issues

Bugs/Instability

• Stabilize GSEA and causal network analysis
• Sometimes plotting clusters on spatially-resolved images (for Xenium data specifically) fails in analysis-specific plots (e.g., combined matrix and UMAP in neighborhood analysis), though can be reliably produced via Spatial.plot_spatial.

Band-Aids to Be Replaced Later

• For now, in order to make Squidpy plotting work, image information for Xenium data is duplicated in Spatial.adata.table/Spatial.rna. under .uns["spatial"][<LIBRARY_ID>]["images"]. When the , we'll want to de-duplicate that (retaining only in Spatial.adata.images) once Squidpy implements full support for spatialdata.SpatialData objects (which they have underway).

Short-Term Plans Not Yet Implemented

• Implementation of CRISPR targetting efficiency calculation
• Ligand-receptor analysis that incorporates spatial information