# Spatial transcriptomics

```{toctree}
:maxdepth: 1

ResolVI to address noise and biases in spatial transcriptomics. <https://scviva-tools.readthedocs.io/en/latest/tutorials/resolVI_tutorial.html>
scVIVA for representing cells and their environment in spatial transcriptomics <https://scviva-tools.readthedocs.io/en/latest/tutorials/scVIVA_tutorial.html>
Multi-resolution deconvolution of spatial transcriptomics <https://scviva-tools.readthedocs.io/en/latest/tutorials/DestVI_tutorial.html>
Introduction to gimVI <https://scviva-tools.readthedocs.io/en/latest/tutorials/gimvi_tutorial.html>
Spatial mapping with Tangram <https://scviva-tools.readthedocs.io/en/latest/tutorials/tangram_scvi_tools.html>
Stereoscope applied to left ventricule data <https://scviva-tools.readthedocs.io/en/latest/tutorials/stereoscope_heart_LV_tutorial.html>
Mapping human lymph node cell types to 10X Visium with Cell2location <https://scviva-tools.readthedocs.io/en/latest/tutorials/cell2location_lymph_node_spatial_tutorial.html>
```

```{customcard}
:path: https://scviva-tools.readthedocs.io/en/latest/tutorials/resolVI_tutorial.html
:title: resolVI: Correcting Noise and Bias in Spatial Transcriptomics
:tags: Analysis, Integration, Transfer-learning, Dimensionality-reduction

Use resolVI to correct cellular-resolved spatial transcriptomics data.
```

```{customcard}
:path: https://scviva-tools.readthedocs.io/en/latest/tutorials/scVIVA_tutorial.html
:title: scVIVA: Representing Cells and Their Spatial Environment
:tags: Analysis, Integration, Dimensionality-reduction, Differential-comparison

Stratify spatial transcriptomics data into niche-aware cell states with scVIVA
```

```{customcard}
:path: https://scviva-tools.readthedocs.io/en/latest/tutorials/DestVI_tutorial.html
:title: DestVI: Multi-Resolution Deconvolution of Spatial Transcriptomics
:tags: Deconvolution, Modality-imputation, Differential-comparison

Perform multi-resolution analysis on spatial transcriptomics data with DestVI
```

```{customcard}
:path: https://scviva-tools.readthedocs.io/en/latest/tutorials/gimvi_tutorial.html
:title: gimVI: Imputing Missing Spatial Genes
:tags: Modality-imputation, Integration

Use gimVI to impute missing genes in spatial data
```

```{customcard}
:path: https://scviva-tools.readthedocs.io/en/latest/tutorials/tangram_scvi_tools.html
:title: Tangram: Mapping Single Cells onto Spatial Data
:tags: Deconvolution, Analysis

Use Tangram to map spatial transcriptomics data
```

```{customcard}
:path: https://scviva-tools.readthedocs.io/en/latest/tutorials/stereoscope_heart_LV_tutorial.html
:title: Stereoscope: Deconvolving Spatial Heart Data
:tags: Deconvolution, Integration

Go through the Stereoscope workflow to map single-cell data
```

```{customcard}
:path: https://scviva-tools.readthedocs.io/en/latest/tutorials/cell2location_lymph_node_spatial_tutorial.html
:title: Cell2location: Mapping Cell Types to Spatial Data
:tags: Dev, Analysis, Integration

Spatially map lymph node cell types using Cell2location
```