AlexsLemonade / AlexsLemonade/scpcaTools

Add demuxmix functions

Open
#282 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
R
Stars
1
Forks
0
PR merge metrics
No merged PRs in 30d

Description

Since we last looked at demultiplexing methods, a number of new methods and packages have come out that we might want to look into. As a first step, we can add functions to perform different multiplexing methods to scpcaTools.

The first of these we might want to look at is [`demuxmix`](https://bioconductor.org/packages/release/bioc/html/demuxmix.html), which uses a mixture model to better model the hashtag oligos. This method performed well in a recent review paper: [Howett et al. 2023](https://doi.org/10.1093/nargab/lqad086).

Following this addition, we can do some evaluations to see if we will want to add this method to `scpca-nf`.

Contributor guide

Open the contributing guide

Research direction

Review the existing demultiplexing functions in scpcaTools and the demuxmix package documentation first. Add the requested demuxmix functions and verify that they support the intended hashtag-oligo mixture-model workflow; evaluation for scpca-nf is explicitly a later step.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
bioinformatics
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.