nichenet_expression_data {OmnipathR} | R Documentation

## 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"

[Package OmnipathR version 3.2.0 Index]