From 13f71b0dae56311e42ee3cb471275d24c8a76b34 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 10 Jan 2025 12:28:14 -0600 Subject: [PATCH] update readme --- analyses/cell-type-ewings/exploratory_analysis/README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/analyses/cell-type-ewings/exploratory_analysis/README.md b/analyses/cell-type-ewings/exploratory_analysis/README.md index 6ee755a3e..f9c78edcc 100644 --- a/analyses/cell-type-ewings/exploratory_analysis/README.md +++ b/analyses/cell-type-ewings/exploratory_analysis/README.md @@ -20,6 +20,9 @@ This includes comparing annotations to those obtained from marker gene annotatio 5. `05-cluster-exploration.Rmd`: This notebook looks at clustering across different parameters to choose the most optimal clusters for `SCPCL000822` and `SCPCL000824`. Additionally, we look at expression of marker genes from `references/visser-all-marker-genes.tsv` across all clusters and use that to refine tumor cell annotations obtained from running `aucell-singler-annotation.sh`. +6. `06-tumor-cell-state-assignments.Rmd`: This notebook looks at assigning tumor cell states in `SCPCL000822` and `SCPCL000824`. +Tumor cells are gruoped into `EWS-FLI` high, `EWS-FLI` low, and `EWS-FLI` middle based on expression of marker genes. + ## Annotation notebooks The `annotation_notebooks` folder contains exploratory notebooks used to explore and validate annotations in individual samples.