Comments (1)
govekk
commented on June 8, 2024
I recently updated the STvEA GitHub to include an example importing data from an FCS file, as well as two functions for reading in FCS files (ReadNamesFCS and ReadDataFCS, both in R/objects.R), which use the flowCore package’s functions for loading an FCS file.
I’ve found that those functions work well for FCS files from both CyTOF and CODEX, but if yours is formatted differently you may find it easier to just copy and tweak the code within the functions for your use.
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Related Issues (13)
- seurat v3+ HOT 1
- CODEX input HOT 7
- Different marker distributions between samples HOT 1
- Normalization of CODEX data HOT 1
- Shiny app source code HOT 1
- Error during 'stvea_object <- GetTransferMatrix(stvea_object)' HOT 6
- Error during MapCODEXtoCITE() HOT 5
- How to map the UMAP result into CODEX spatial figure ? HOT 1
- Color legend to interpret the colors in the heatmap (CODEX protein adj map & cluster adj map) HOT 1
- I can't reproduce your example HOT 1
- AdjScoreProteins errors: adjacency score for each feature pairError: $ operator is invalid for atomic vectors HOT 8
- CleanCODEX() error HOT 5
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