nichenet_expression_data {OmnipathR} | R Documentation |
NicheNet uses expression data from a collection of published ligand or receptor KO or perturbation experiments to build its model. This function retrieves the original expression data, deposited in Zenodo (https://zenodo.org/record/3260758).
nichenet_expression_data()
Nested list, each element contains a data frame of processed expression data and key variables about the experiment.
exp_data <- nichenet_expression_data() head(names(exp_data)) # [1] "bmp4_tgfb" "tgfb_bmp4" "nodal_Nodal" "spectrum_Il4" # [5] "spectrum_Tnf" "spectrum_Ifng" purrr::map_chr(head(exp_data), 'from') # bmp4_tgfb tgfb_bmp4 nodal_Nodal spectrum_Il4 spectrum_Tnf # "BMP4" "TGFB1" "NODAL" "IL4" "TNF" # spectrum_Ifng # "IFNG"