AlexsLemonade / AlexsLemonade/OpenScPCA-analysis

Record project-specific normal reference groups in TSVs

Open
#1,239 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
HTML
Stars
16
Forks
24
Avg merge
3d 5h
Merged PRs (30d)
4

Description

> Ultimately I think we want to have a TSV file with the project ID and then a column for the groups to create and the cell types that should be included in the normal group. That will make it easier to process across all projects and track down which groups are used where. I don't think we need that in this PR but we might file an issue to do that later?

_Originally posted by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1169#discussion_r2231898615_

Edit: Noting this parallel comment, https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1169#discussion_r2231899596

---

The goal of this issue is to add TSVs into the `infercnv-consensus-cell-type` module that provide the normal reference groups for each project. We'll also need to update `scripts/build-normal-references.R` parse a TSV input with that information instead of direct taking arguments for reference cell groupings.

Contributor guide

Open the contributing guide

Research direction

Start by inspecting the infercnv-consensus-cell-type module and scripts/build-normal-references.R. Trace how normal reference cell groupings are currently passed, then review the existing project metadata TSV conventions. Done means project-specific TSVs provide the groups and included cell types, and the script parses that information instead of direct grouping arguments.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
bioinformatics, data
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.