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All Projects → ismms-himc → visium-clustergrammer2

ismms-himc / visium-clustergrammer2

Licence: BSD-3-Clause License
Spatial Transcriptomics Dashboard

Programming Languages

Jupyter Notebook
11667 projects
python
139335 projects - #7 most used programming language

Labels

webgljupyterheatmapscrna-seqvoilavisium

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Visium-Clustergrammer2

Binder

visium-clustergrammer2

Data

10X Visium Dataset

The 10X Visium data was obtained from from 10x Genomics. The data was not included in this repo because of GitHub size limitations but can be easily obtained from 10x Genomics Datasets.

Reference Dataset

Similarly to the Seurat spatial vignette we used a single cell RNA-seq dataset (~14,000 Mouse cortical cells produced by the Allen Institute) as a reference dataset for labeling the Visium data.

References

This project was influenced by the Seurat spatial vignette from the Satija lab and we are very grateful for thier public examples.

MyBinder link

Contributors

Nicolas Fernandez

Assaf Magen

Adeeb Rahman

Manuel Garcia-Quismondo

Tutorial Video

visium-clustergrammer2

Contact and Feedback

Please contact us through the Gitter Discussion Board or issue tracker with questions comments or concerns.

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