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fsdecode

This package enables gene expression decoding using various models. It relies on the python toolboxes BrainSMASH and neuromaps, which have to be installed prior to the fsdecode package. Also, it relies on the R package fsnulls, which can be installed from GitHub.

Installation

First, install the fsnulls package from GitHub.

Then, specify the path to the python interpreter in the .Rprofile file, e.g.,

if (benchmarkme::get_cpu()$model_name == "Apple M1 Max") {
  Sys.setenv(RETICULATE_PYTHON = "/Users/sphache/miniconda3/bin/python")
} else {
  Sys.setenv(RETICULATE_PYTHON = "/opt/anaconda3/bin/python")
}

library(reticulate)
reticulate::py_config()

or

python.path <- "/opt/anaconda3/bin/python"
reticulate::use_python(python.path)

Downloading the repository

Given the large amount of metadata that is contained within the package, it uses git annex to store the data on a remove repository other than github. You therefore also need to install datalad, which can be used to clone the repository and to download the data.

To clone the repository, use

datalad clone https://github.com/christineecker/fsdecode.git

To download the data, use

datalad get data/
datalad get inst/extdata
# etc.