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Add spatial transcriptomics tools to Single-cell section #18

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Add spatial transcriptomics tools to Single-cell section #18

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Expand Up @@ -1817,6 +1817,10 @@ Semi-global alignment is global alignment with an optional gap at the end(s).
- Topological analysis: https://github.com/RabadanLab/scTDA
- Deconvolution of bulk RNA from scRNA: https://github.com/xuranw/MuSiC
- Minimum metadata for reporting scRNA-seq experiments: https://arxiv.org/abs/1910.14623
- Spatial transcriptomics
- DeepSpot-M: multimodal foundation model for transcriptome-wide prediction of spatial expression from H&E histology; genes are queryable embeddings rather than fixed outputs https://github.com/ratschlab/DeepSpotM
- DeepSpot: prediction of spot-level (Visium) and single-cell (Xenium) spatial expression from H&E images https://github.com/ratschlab/DeepSpot
- AESTETIK: representation learning over expression, tissue morphology and spatial context for spatial domain identification https://github.com/ratschlab/aestetik
- DNA-seq
- haplotype inference: https://github.com/raphael-group/chisel
- ATAC-seq
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