AlexsLemonade / AlexsLemonade/sc-data-integration

Function to calculate IDER-based metric

Open
#88 6 comments 0 reactions 0 assignees View on GitHub
Dominant language
HTML
Stars
0
Forks
0
PR merge metrics
No merged PRs in 30d

Description

We should write a function that takes an integrated SCE object and calculates the IDER-based metric. The final output from this function should be an R object that can be saved to file, likely either TSV or RDS depending on the specific content of the calculations.

References:
- "Quick start" from the R package README: https://github.com/zhiyhu/CIDER#cider-as-an-evaluation-metric---quick-start
- Vignette: https://zhiyhu.github.io/CIDER/articles/evaluation.html

As described in the references above, the input will need to be a `Seurat` object, so this function will need to convert SCE --> Seurat to begin.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with the CIDER Quick start in the R package README and the evaluation vignette linked in the issue to understand the required metric inputs and outputs. Then inspect the existing SCE-to-Seurat conversion entry point, if present; done means a function accepts the integrated SCE object, computes the IDER-based metric, and returns a savable R object.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.