Skip to content

Recache OmnipathR to avoid deCoupler issue #314

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
bbimber wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Recache OmnipathR to avoid deCoupler issue #314

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
02b7a88
Recache OmnipathR to avoid deCoupler issue
bbimber Jul 29, 2026
05eff9f
Bugfix
bbimber Jul 29, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 12 additions & 9 deletions tests/testthat/test-decoupleR.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,18 @@ context("scRNAseq")
test_that("RunDecoupleR works as expected", {
# This failed on github runners with a non-informative 'job terminated' error.
if (version$minor > 4.3) {
# TODO: disabled due to decoupleR::get_collectri error
# seuratObj <- suppressWarnings(Seurat::UpdateSeuratObject(readRDS('../testdata/seuratOutput.rds')))
# seuratObj <- RunDecoupleR(seuratObj)
#
# expect_true('tfsulm' %in% names(seuratObj@assays))
# expect_equal(nrow(seuratObj@assays$tfsulm), 726)
# expect_equal(ncol(seuratObj@assays$tfsulm), ncol(seuratObj))
#
# CellMembrane::PlotTfData(seuratObj, groupField = 'Phase')
# See: https://github.com/saezlab/OmnipathR/issues/127#issuecomment-5111448160
OmnipathR::omnipath_cache_wipe()
invisible(OmnipathR::collectri())

seuratObj <- suppressWarnings(Seurat::UpdateSeuratObject(readRDS('../testdata/seuratOutput.rds')))
seuratObj <- RunDecoupleR(seuratObj)

expect_true('tfsulm' %in% names(seuratObj@assays))
expect_equal(nrow(seuratObj@assays$tfsulm), 726)
expect_equal(ncol(seuratObj@assays$tfsulm), ncol(seuratObj))

CellMembrane::PlotTfData(seuratObj, groupField = 'Phase')
} else {
print('Skipping decoupleR tests')
}
Expand Down
Loading