This workflow requires file inputs to be stored on Synapse. It is free to make an account and store small files. Store your counts files and metadata on Synapse.
Specify the active configuration by setting R_CONFIG_ACTIVE.
profile_set <- "default"
Sys.setenv(R_CONFIG_ACTIVE = profile_set)Store your Synapse credentials locally. You can achieve this by either creating a .synapseConfig file or executing synLogin() with rememberMe = True. If you are working inside a Docker, make a text file called .synapseConfig from the home directory inside your container. This article describes the format of the .synapseConfig file.
Load the sageseqr library. start_de() copies the targets plan to your working directory. Execute targets::make() to compute. Run this code from your project root.
library(sageseqr)
library(targets)
# gather the dependencies in your working directory by running this function:
start_de()
# inspect the steps of the workflow
tar_manifest()
# run the analysis
tar_make()