From db883e5525ee2c6f0c6fd9f70ef5b2167c6e3b5d Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Fri, 3 Jan 2025 15:41:52 -0600 Subject: [PATCH] link to reference instructions --- analyses/cell-type-consensus/README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/analyses/cell-type-consensus/README.md b/analyses/cell-type-consensus/README.md index b4bf29d9b..3346815b9 100644 --- a/analyses/cell-type-consensus/README.md +++ b/analyses/cell-type-consensus/README.md @@ -8,7 +8,8 @@ Specifically, the cell type annotations obtained from both `SingleR` and `CellAs The goal of this module is to create a reference that can be used to define an ontology aware consensus cell type label for all cells across all ScPCA samples. This module performs a series of steps to accomplish that goal: -1. The cell type annotations present in the `PanglaoDB` reference file were assigned to an ontology term identifier, when possible. +1. The cell type annotations present in the `PanglaoDB` reference file were assigned to an ontology term identifier, when possible. +See [`references/README.md`](./references/README.md) for a full description on how we completed assignments. 2. We looked at all possible combinations of cell type labels between the `PanglaoDB` reference (used with `CellAssign`) and the `BlueprintEncodeData` reference (used with `SingleR`). We then explored using a set of rules used to define consensus cell types in [`exploratory-notebooks/01-reference-exploration.Rmd`](./exploratory-notebooks/01-reference-exploration.Rmd). 3. We created a [reference table](./references/consensus-cell-type-reference.tsv) containing all combinations for which we were able to identify a consensus cell type label.