Add tutorials covering SpatialData, SnapATAC2, pertpy, LIANA+, scirpy BCR and decoupler (#298)

* Add tutorials covering SpatialData, SnapATAC2, pertpy, LIANA+, scirpy BCR and decoupler

Three core packages had no presence on /learn at all: SpatialData, SnapATAC2
and pertpy. This adds an entry point for each, plus tutorials that fill gaps
inside packages that were already listed.

Adds a Cell-cell communication category, which had no coverage, and fills the
Multimodal category, which was defined but empty and therefore never rendered.

* Shorten descriptions so they are not clipped on the cards

Author: Zethson

tutorial-registry/categories.yml

@@ -16,6 +16,10 @@
     description: |
       Tutorials for analyzing single-cell B-cell and T-cell receptor sequencing data
 
+- Cell-cell communication:
+    description: |
+      Infer and analyse interactions between cells
+
 - Surface proteins:
     description: |
       CITE-seq analyses

tutorial-registry/schema.json

@@ -31,6 +31,7 @@
                 "scRNA-seq",
                 "Spatial",
                 "Adaptive immune cell receptor",
+                "Cell-cell communication",
                 "Surface proteins",
                 "ATAC-seq",
                 "Multimodal",

tutorial-registry/tutorials/decoupler-single-cell-enrichment/icon.png

@@ -0,0 +1,18 @@
+name: Single-cell enrichment analysis
+description: |
+  Score transcription factor and pathway activities per cell, then compare them across cell types.
+link: https://decoupler.readthedocs.io/en/latest/notebooks/scell/rna_sc.html
+image: icon.png
+primary_category: scRNA-seq
+order: 25
+modality:
+  - RNA
+tags:
+  - functional analysis
+  - visualization
+packages:
+  - decoupler
+  - scanpy
+  - anndata
+authors:
+  - PauBadiaM

tutorial-registry/tutorials/decoupler-single-cell-enrichment/meta.yaml

@@ -0,0 +1,18 @@
+name: Cell-cell communication with LIANA+
+description: |
+  Infer ligand-receptor interactions between cell types and aggregate the methods into a consensus ranking.
+link: https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html
+image: icon.png
+primary_category: Cell-cell communication
+order: 10
+modality:
+  - RNA
+tags:
+  - functional analysis
+  - visualization
+packages:
+  - liana
+  - scanpy
+  - anndata
+authors:
+  - dbdimitrov

tutorial-registry/tutorials/liana-ligand-receptor/icon.png

@@ -0,0 +1,19 @@
+name: Perturbation efficacy in pooled CRISPR screens
+description: |
+  Find which cells in a pooled CRISPR screen were effectively perturbed, with Mixscape and Mixscale.
+link: https://pertpy.readthedocs.io/en/latest/tutorials/notebooks/perturbation_efficacy.html
+image: icon.svg
+primary_category: scRNA-seq
+order: 110
+modality:
+  - RNA
+tags:
+  - perturbation
+  - quality control
+  - visualization
+packages:
+  - pertpy
+  - scanpy
+  - anndata
+authors:
+  - Zethson

tutorial-registry/tutorials/liana-ligand-receptor/meta.yaml

@@ -0,0 +1,20 @@
+name: Quantifying perturbation effects with distances
+description: |
+  Measure how strongly a perturbation shifts cells with point-cloud distance metrics and permutation tests.
+link: https://pertpy.readthedocs.io/en/latest/tutorials/notebooks/distances.html
+image: icon.svg
+primary_category: scRNA-seq
+order: 90
+modality:
+  - RNA
+tags:
+  - perturbation
+  - visualization
+packages:
+  - pertpy
+  - scanpy
+  - anndata
+authors:
+  - stefanpeidli
+  - Lilly-May
+  - Zethson