diff --git a/tutorial-registry/categories.yml b/tutorial-registry/categories.yml index ffb7b99..e4258b4 100644 --- a/tutorial-registry/categories.yml +++ b/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 diff --git a/tutorial-registry/schema.json b/tutorial-registry/schema.json index 60ae5d1..5bd9b14 100644 --- a/tutorial-registry/schema.json +++ b/tutorial-registry/schema.json @@ -31,6 +31,7 @@ "scRNA-seq", "Spatial", "Adaptive immune cell receptor", + "Cell-cell communication", "Surface proteins", "ATAC-seq", "Multimodal", diff --git a/tutorial-registry/tutorials/decoupler-single-cell-enrichment/icon.png b/tutorial-registry/tutorials/decoupler-single-cell-enrichment/icon.png new file mode 100644 index 0000000..f9032ef Binary files /dev/null and b/tutorial-registry/tutorials/decoupler-single-cell-enrichment/icon.png differ diff --git a/tutorial-registry/tutorials/decoupler-single-cell-enrichment/meta.yaml b/tutorial-registry/tutorials/decoupler-single-cell-enrichment/meta.yaml new file mode 100644 index 0000000..9c0bf99 --- /dev/null +++ b/tutorial-registry/tutorials/decoupler-single-cell-enrichment/meta.yaml @@ -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 diff --git a/tutorial-registry/tutorials/liana-ligand-receptor/icon.png b/tutorial-registry/tutorials/liana-ligand-receptor/icon.png new file mode 100644 index 0000000..a203df0 Binary files /dev/null and b/tutorial-registry/tutorials/liana-ligand-receptor/icon.png differ diff --git a/tutorial-registry/tutorials/liana-ligand-receptor/meta.yaml b/tutorial-registry/tutorials/liana-ligand-receptor/meta.yaml new file mode 100644 index 0000000..cbd892b --- /dev/null +++ b/tutorial-registry/tutorials/liana-ligand-receptor/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 diff --git a/tutorial-registry/tutorials/pertpy-crispr-perturbation-efficacy/icon.svg b/tutorial-registry/tutorials/pertpy-crispr-perturbation-efficacy/icon.svg new file mode 100644 index 0000000..0ca3d53 --- /dev/null +++ b/tutorial-registry/tutorials/pertpy-crispr-perturbation-efficacy/icon.svg @@ -0,0 +1,4 @@ + + + + diff --git a/tutorial-registry/tutorials/pertpy-crispr-perturbation-efficacy/meta.yaml b/tutorial-registry/tutorials/pertpy-crispr-perturbation-efficacy/meta.yaml new file mode 100644 index 0000000..18eab13 --- /dev/null +++ b/tutorial-registry/tutorials/pertpy-crispr-perturbation-efficacy/meta.yaml @@ -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 diff --git a/tutorial-registry/tutorials/pertpy-perturbation-distances/icon.svg b/tutorial-registry/tutorials/pertpy-perturbation-distances/icon.svg new file mode 100644 index 0000000..0ca3d53 --- /dev/null +++ b/tutorial-registry/tutorials/pertpy-perturbation-distances/icon.svg @@ -0,0 +1,4 @@ + + + + diff --git a/tutorial-registry/tutorials/pertpy-perturbation-distances/meta.yaml b/tutorial-registry/tutorials/pertpy-perturbation-distances/meta.yaml new file mode 100644 index 0000000..3f3ed39 --- /dev/null +++ b/tutorial-registry/tutorials/pertpy-perturbation-distances/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 diff --git a/tutorial-registry/tutorials/pertpy-perturbation-space/icon.svg b/tutorial-registry/tutorials/pertpy-perturbation-space/icon.svg new file mode 100644 index 0000000..0ca3d53 --- /dev/null +++ b/tutorial-registry/tutorials/pertpy-perturbation-space/icon.svg @@ -0,0 +1,4 @@ + + + + diff --git a/tutorial-registry/tutorials/pertpy-perturbation-space/meta.yaml b/tutorial-registry/tutorials/pertpy-perturbation-space/meta.yaml new file mode 100644 index 0000000..faeb0a4 --- /dev/null +++ b/tutorial-registry/tutorials/pertpy-perturbation-space/meta.yaml @@ -0,0 +1,19 @@ +name: Perturbation spaces +description: | + Summarize all cells of a perturbation into a single point, to compare whole perturbations rather than cells. +link: https://pertpy.readthedocs.io/en/latest/tutorials/notebooks/perturbation_space.html +image: icon.svg +primary_category: scRNA-seq +order: 100 +modality: + - RNA +tags: + - perturbation + - visualization +packages: + - pertpy + - scanpy + - anndata +authors: + - Lilly-May + - Zethson diff --git a/tutorial-registry/tutorials/scirpy-bcr/icon.svg b/tutorial-registry/tutorials/scirpy-bcr/icon.svg new file mode 100644 index 0000000..12a5085 --- /dev/null +++ b/tutorial-registry/tutorials/scirpy-bcr/icon.svg @@ -0,0 +1,146 @@ + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + diff --git a/tutorial-registry/tutorials/scirpy-bcr/meta.yaml b/tutorial-registry/tutorials/scirpy-bcr/meta.yaml new file mode 100644 index 0000000..dea2de9 --- /dev/null +++ b/tutorial-registry/tutorials/scirpy-bcr/meta.yaml @@ -0,0 +1,20 @@ +name: B-cell receptor analysis with scirpy +description: | + Quality control, clonotype definition, somatic hypermutation and isotype usage in 5k B cells. +link: https://scirpy.scverse.org/en/latest/tutorials/tutorial_5k_bcr.html +image: icon.svg +primary_category: Adaptive immune cell receptor +order: 20 +modality: + - AIRR + - RNA +tags: + - quality control + - preprocessing + - visualization +packages: + - scirpy + - mudata + - anndata +authors: + - grst diff --git a/tutorial-registry/tutorials/snapatac2-multiome/icon.svg b/tutorial-registry/tutorials/snapatac2-multiome/icon.svg new file mode 100644 index 0000000..6bd807c --- /dev/null +++ b/tutorial-registry/tutorials/snapatac2-multiome/icon.svg @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + ® + diff --git a/tutorial-registry/tutorials/snapatac2-multiome/meta.yaml b/tutorial-registry/tutorials/snapatac2-multiome/meta.yaml new file mode 100644 index 0000000..113e6c4 --- /dev/null +++ b/tutorial-registry/tutorials/snapatac2-multiome/meta.yaml @@ -0,0 +1,20 @@ +name: Single-cell multiome analysis with SnapATAC2 +description: | + Analyze paired ATAC and gene expression from a 10x multiome experiment in a joint embedding. +link: https://snapatac2.scverse.org/tutorials/modality.html +image: icon.svg +primary_category: Multimodal +order: 10 +modality: + - ATAC + - RNA +tags: + - multimodal + - data integration + - preprocessing +packages: + - snapatac2 + - scanpy + - anndata +authors: + - kaizhang diff --git a/tutorial-registry/tutorials/snapatac2-pbmc/icon.svg b/tutorial-registry/tutorials/snapatac2-pbmc/icon.svg new file mode 100644 index 0000000..6bd807c --- /dev/null +++ b/tutorial-registry/tutorials/snapatac2-pbmc/icon.svg @@ -0,0 +1,40 @@ + + + + + + + + + + + + + + + ® + diff --git a/tutorial-registry/tutorials/snapatac2-pbmc/meta.yaml b/tutorial-registry/tutorials/snapatac2-pbmc/meta.yaml new file mode 100644 index 0000000..9d0ef6e --- /dev/null +++ b/tutorial-registry/tutorials/snapatac2-pbmc/meta.yaml @@ -0,0 +1,19 @@ +name: Standard scATAC-seq pipeline with SnapATAC2 +description: | + From fragment file to annotated clusters on 5k PBMCs: quality control, dimension reduction, clustering. +link: https://snapatac2.scverse.org/tutorials/pbmc.html +image: icon.svg +primary_category: ATAC-seq +order: 5 +modality: + - ATAC +tags: + - quality control + - preprocessing + - cell-type annotation + - visualization +packages: + - snapatac2 + - anndata +authors: + - kaizhang diff --git a/tutorial-registry/tutorials/spatialdata-intro/icon.svg b/tutorial-registry/tutorials/spatialdata-intro/icon.svg new file mode 100644 index 0000000..728efc5 --- /dev/null +++ b/tutorial-registry/tutorials/spatialdata-intro/icon.svg @@ -0,0 +1,108 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tutorial-registry/tutorials/spatialdata-intro/meta.yaml b/tutorial-registry/tutorials/spatialdata-intro/meta.yaml new file mode 100644 index 0000000..3cb2f62 --- /dev/null +++ b/tutorial-registry/tutorials/spatialdata-intro/meta.yaml @@ -0,0 +1,17 @@ +name: Introduction to SpatialData +description: | + A tour of the SpatialData object: images, labels, points, shapes, tables and coordinate systems. +link: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/intro.html +image: icon.svg +primary_category: Data structures +order: 60 +modality: + - spatial +tags: + - data structures + - visualization +packages: + - spatialdata + - anndata +authors: + - LucaMarconato diff --git a/tutorial-registry/tutorials/spatialdata-xenium/icon.svg b/tutorial-registry/tutorials/spatialdata-xenium/icon.svg new file mode 100644 index 0000000..728efc5 --- /dev/null +++ b/tutorial-registry/tutorials/spatialdata-xenium/icon.svg @@ -0,0 +1,108 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tutorial-registry/tutorials/spatialdata-xenium/meta.yaml b/tutorial-registry/tutorials/spatialdata-xenium/meta.yaml new file mode 100644 index 0000000..0ba3e9a --- /dev/null +++ b/tutorial-registry/tutorials/spatialdata-xenium/meta.yaml @@ -0,0 +1,20 @@ +name: Reading Xenium data with SpatialData +description: | + Read a 10x Genomics Xenium experiment and explore transcripts, cell boundaries and morphology images. +link: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/technology_xenium.html +image: icon.svg +primary_category: Spatial +order: 5 +modality: + - spatial + - RNA +tags: + - data structures + - preprocessing + - visualization +packages: + - spatialdata + - spatialdata-io +authors: + - LucaMarconato + - giovp