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Spatially-resolved Transcriptomics via Epitope Anchoring
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README.md

README.md

STvEA

STvEA is an analysis pipeline for cleaning, clustering, and plotting CODEX and CITE-seq protein data, mapping a CODEX dataset to a matching CITE-seq dataset, and assessing colocalization of features using the Adjacency Score.

Installation

devtools::install_github("CamaraLab/STvEA")

Tutorials

Analyzing CODEX data

Example pipeline for only CODEX data. Performs filtering of protein expression data, visualization of clusters, and analysis of the spatial co-localization of both clusters and proteins.

Mapping CODEX data to CITE-seq data

Performs separate filtering and clustering for both CODEX and CITE-seq protein expression data. Maps the CODEX protein space to the CITE-seq protein space in order to transfer features such as gene expression and clusters from the CITE-seq cells onto the CODEX cells. Analyzes co-localization of genes, proteins, and clusters using the Adjacency Score.

Mapping CODEX data to CITE-seq data analyzed using Seurat

Retrieves information about the CITE-seq mRNA and protein expression data from a Seurat object. Performs separate filtering and clustering for both CODEX and CITE-seq protein expression data. Maps the CODEX protein space to the CITE-seq protein space in order to transfer features such as gene expression and clusters from the CITE-seq cells onto the CODEX cells. Analyzes co-localization of genes, proteins, and clusters using the Adjacency Score.

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