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Home
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About TransImp
===============

TransImp (Translation-based Spatial Transcriptomics Imputation toolkit) is a computational framework and toolbox for reference-based imputation of spatial transcriptomic dataset.

TransImp features in two novel functions: \
 1) Uncertainty score estimation for each imputed gene, allowing the identification of relible predictions; \
 2) Spatial regularisation for explicitily control the degree of spatial pattern preservation for imputation modeling.

The toolkit also includes **TransDeconv**, a translation-based cell-type deconvolution method that infers per-spot cell-type proportions from spatial transcriptomics data using a scRNA-seq reference. As of v0.2, TransDeconv supports an AnnData-based interface with automatic preprocessing, marker gene selection, score-init, cluster-mapping regularization, and JS-divergence loss.

Please refer to our demo notebooks for details:

* `Different configurations of TransImp applied to SeqFISH dataset dataset`_.

* `Exploration for unprobed genes with SeqFISH ST dataset`_.

* `Cell type deconvolution with TransDeconv`_.

.. _Different configurations of TransImp applied to SeqFISH dataset dataset: seqfish.ipynb

.. _Exploration for unprobed genes with SeqFISH ST dataset: seqfish_unprobed_genes.ipynb

.. _Cell type deconvolution with TransDeconv: transDeconv.ipynb



References
==========
Manuscript of TransImp with more details is available on bioRxiv_ now and is currently under review.

.. _bioRxiv: https://www.biorxiv.org/content/10.1101/2023.01.20.524992v1
.. _Patterns: https://www.sciencedirect.com/science/article/pii/S2666389924001545



.. toctree::
   :caption: Main
   :maxdepth: 1
   :hidden:
   
   install
   api
   release

.. toctree::
   :caption: Examples
   :maxdepth: 1
   :hidden:

   seqfish
   seqfish_unprobed_genes
   transDeconv