Last updated: 2024-03-21

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Knit directory: mi_spatialomics/

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File Version Author Date Message
Rmd 56559c7 FloWuenne 2024-03-21 Cleaned up repository.
Rmd f4d5c82 FloWuenne 2024-01-15 Latest update to Seurat analysis with reprocessed data.
Rmd 2d9b909 FloWuenne 2024-01-09 Pushing latest changes. Updating molkart data.
html 2d9b909 FloWuenne 2024-01-09 Pushing latest changes. Updating molkart data.
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html 3b5ca40 FloWuenne 2023-06-12 Added code for supplementary Figures.
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Rmd 62020bf FloWuenne 2023-06-12 Configure site header.

Molecular Cartography

Processing of raw data

The raw Molecular Cartography data was processed using the nf-core/molkart pipeline (revision: 81eafe9f9993d4daf16371ba3804ce9ae08053ad). The configurations, parameters and models used to reproduce the processing can be found in : ./pipeline_configs/nf-core_molkart.

All downstream processing after nf-core/molkart was performed in R and Python using scripts provided and documented in this repository. See Data analysis - Molecular Cartography for more details.

Sequential Immunofluorescence

Raw Lunaphore images were processed using MCMICRO. The configurations, parameters and commands used can be found in : ./pipeline_configs/mcmicro.

Downstream processing after MCMICRO was performed in R and Python using scripts provided and documented in this repository. See Data analysis - SeqIF for more details.