Last updated: 2024-11-02

Checks: 2 0

Knit directory: spatialsnippets/

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File	Version	Author	Date	Message
Rmd	1749950	swbioinf	2024-11-02	wflow_publish("analysis/")
html	2b1c8e2	swbioinf	2024-09-19	Build site.
Rmd	511594f	swbioinf	2024-09-19	wflow_publish("analysis/")
html	5347093	swbioinf	2024-09-17	Build site.
Rmd	7eec547	swbioinf	2024-09-17	wflow_publish("analysis/")
html	2e26929	Sarah Williams	2024-03-25	Build site.
Rmd	0a3a1ae	Sarah Williams	2024-03-25	wflow_publish("analysis/")
html	30da140	Sarah Williams	2024-03-22	Build site.
Rmd	89c3371	Sarah Williams	2024-03-22	wflow_publish(c("analysis/index_data.Rmd", "analysis/index.Rmd",
html	bd24df4	Sarah Williams	2023-11-01	Build site.
Rmd	8b1c005	Sarah Williams	2023-11-01	wflow_publish("analysis")
html	e7a4c12	Sarah Williams	2023-10-18	Build site.
Rmd	507ead4	Sarah Williams	2023-10-18	wflow_publish("analysis/")

These examples assume that the data has been loaded, preprocessed (e.g. QC-ed, UMAP) and annotated (e.g. sample names, cell types, cell niches). For information, the preprocessing applied here is included in data preparation below. Please note that these are not full annotations, and do not aim to reproduce the authors’ published analyses! These are simplified and rough annotations to enable running these tests.

References

Garrido-Trigo, Alba, Ana M. Corraliza, Marisol Veny, Isabella Dotti, Elisa Melón-Ardanaz, Aina Rill, Helena L. Crowell, et al. 2023. “Macrophage and Neutrophil Heterogeneity at Single-Cell Spatial Resolution in Human Inflammatory Bowel Disease.” Nature Communications 14 (1): 4506. https://doi.org/10.1038/s41467-023-40156-6.

Mallach, Anna, Magdalena Zielonka, Veerle van Lieshout, Yanru An, Jia Hui Khoo, Marisa Vanheusden, Wei-Ting Chen, et al. 2024. “Microglia-Astrocyte Crosstalk in the Amyloid Plaque Niche of an Alzheimer’s Disease Mouse Model, as Revealed by Spatial Transcriptomics.” Cell Reports 43 (6): 114216. https://doi.org/10.1016/j.celrep.2024.114216.

Moreau, Julie L. M., Sarah Williams, Jihane Homman-Ludiye, Andrew J. Mallett, and Alexander N. Combes. 2023. “Forming Nephrons Promote Nephron Progenitor Maintenance and Branching Morphogenesis via Paracrine BMP4 Signalling Under the Control of Wnt4.” https://doi.org/10.1101/2023.11.19.567482.

Data

References