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FredHutch / Galeano-Nino-Bullman-Intratumoral-Microbiota_2022

Analysis code used in Galeano Nino et al., Impact of Intratumoral Microbiota on Spatial and Cellular Heterogeneity in human cancer. 2022
MIT License
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Availability of Seurat objs #6

Closed MathiniVaikunthan closed 1 year ago

MathiniVaikunthan commented 1 year ago

Is the best way of obtaining the Seurat objs for the 0, 100, 500 MOI experiment in HCT116 to download all of the separate sequencing runs and go through the cell_culture_Seurat.r pipeline or is the output gene expression object stored somewhere? Thank you

hanruiw commented 1 year ago

Hi, the expression matrix is not uploaded, so the best way to obtain the R object is to process the raw fastq files. Please let me know if you have any questions!