GitHub - Nanostring-Biostats/Insitutype-manuscript-analyses: Analyses for the manuscript, "Insitutype: likelihood-based cell typing for single cell spatial transcriptomics"

This repo holds analyses used in the manuscript, "Insitutype: likelihood-based cell typing for single cell spatial transcriptomics".

Note: the datasets used here are too big to host on github. They can be downloaded from: https://nanostring.box.com/s/cx5j3dlrmext3guyy1bb2r4rm6p8d364.

How to use:

First, download the data from the above url and place in the "data" folder.
Each folder holds a distinct analysis (a figure or sub-figure)
All R scripts execute in the directory in which they lie
These analyses use a development version of Insitutype, "MLEcell". This package can be installed using the "environment_setup" script.
The benchmarking analysis (Fig 4) uses a more final version of the package, "InSituType". This is also installed in the "environment_setup" script.

Name		Name	Last commit message	Last commit date
Latest commit History 6 Commits
Fig 2ab - NB assumptions		Fig 2ab - NB assumptions
Fig 2c - posterior probabilities		Fig 2c - posterior probabilities
Fig 3cd - cohorting in kidney		Fig 3cd - cohorting in kidney
Fig 4 - benchmarking analysis		Fig 4 - benchmarking analysis
Fig 5 - demo in kidney		Fig 5 - demo in kidney
Fig 6 - demo in NSCLC		Fig 6 - demo in NSCLC
Fig S1 - sketching demonstration		Fig S1 - sketching demonstration
Fig S2 - demo in vizgen mouse brain		Fig S2 - demo in vizgen mouse brain
Fig S6 - compare to other spatial transcriptomics clustering methods		Fig S6 - compare to other spatial transcriptomics clustering methods
data		data
.gitattributes		.gitattributes
LICENSE		LICENSE
README.md		README.md

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