From f342d7c12307781c19e5ccb03e74cb682e46fde8 Mon Sep 17 00:00:00 2001 From: Ori Kronfeld Date: Mon, 2 Sep 2024 14:42:23 +0300 Subject: [PATCH] Changes scarches toturial --- scrna/scarches_scvi_tools.ipynb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/scrna/scarches_scvi_tools.ipynb b/scrna/scarches_scvi_tools.ipynb index 2d20f57..7e2669a 100644 --- a/scrna/scarches_scvi_tools.ipynb +++ b/scrna/scarches_scvi_tools.ipynb @@ -297,9 +297,15 @@ "id": "2C37BM-pCM_o" }, "source": [ - "We train the reference using the standard SCVI workflow, except we add a few non-default parameters that were identified to work well with scArches." + "We train the reference using the standard SCVI workflow, except we add a few non-default parameters that were identified to work well with scArches. \n", + "It is essential to encode covariates here as this allows scArches to map new batches in the encoder to the existing data and thereby provides batch integration. " ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, { "cell_type": "code", "execution_count": 11,