nichenet_expression_data: Expression data from ligand-receptor perturbation experiments...

In saezlab/OmnipathR: OmniPath web service client and more

Expression data from ligand-receptor perturbation experiments used by NicheNet

Description

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).

Usage

nichenet_expression_data()

Value

Nested list, each element contains a data frame of processed expression data and key variables about the experiment.

Examples

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"

saezlab/OmnipathR documentation built on May 3, 2024, 5:32 a.m.