Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. michael.skinnider@msl.ubc.ca.
Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada. michael.skinnider@msl.ubc.ca.
Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. jordan.squair@epfl.ch.
NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland. jordan.squair@epfl.ch.
International Collaboration on Repair Discoveries (ICORD), University of British Columbia, Vancouver, British Columbia, Canada. jordan.squair@epfl.ch.
Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
Departments of Physiology and Pharmacology, Clinical Neurosciences, and Cardiac Sciences, Hotchkiss Brain Institute and Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Alberta, Canada.
Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
Brain Mind Institute, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. gregoire.courtine@epfl.ch.
NeuroRestore, Department of Clinical Neuroscience, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland. gregoire.courtine@epfl.ch.
Center for Neuroprosthetics, Faculty of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. gregoire.courtine@epfl.ch.
We present Augur, a method to prioritize the cell types most responsive to biological perturbations in single-cell data. Augur employs a machine-learning framework to quantify the separability of perturbed and unperturbed cells within a high-dimensional space. We validate our method on single-cell RNA sequencing, chromatin accessibility and imaging transcriptomics datasets, and show that Augur outperforms existing methods based on differential gene expression. Augur identified the neural circuits restoring locomotion in mice following spinal cord neurostimulation.
