AlexsLemonade / AlexsLemonade/scpcaTools
Add demuxmix functions
- 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
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