llrs / llrs/experDesign

Help fill out a plate or detect it

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enhancement
Dominant language
R
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Description

If a plate has X positions it would be nice if there were some kind of helper functions to find which samples can go to which positions.
This could help to fill up a batch (when still with time).

Also it could help to find how many plates there are in an experiment and thus help diagnose problems better.
Example taken from the OSCA book:

library(scRNAseq)
sce.seger <- SegerstolpePancreasData()
df <- data.frame(rownames = rownames(colData(sce.seger)), colData(sce.seger))
dfull <- tidyr::separate_wider_delim(df, cols = rownames, delim = "_", names = c("S", "P"))
s <- strcapture("([A-Z])([0-9]*)", proto = data.frame(row = character(), col = character()), x = dfull$P)
s2 <- cbind(dfull, s)

The experiment was done in plates of 24*16 = 384 samples in a plate. Each donor uses less than a full plate. But there are also 14 different Cell types (at most 12 per donor). [Note to self: in the guide they just do mutual nearest neighbors (MNN)]

Was each donor in a plate? Thus making this a batch effect? Or were multiple donors in the same plate thus reducing the batch effect to compare between donors?

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the R example from the OSCA book and the issue's 24×16 plate scenario. Clarify whether the goal is to identify samples and available positions, count plates, investigate donor placement, or all three; done should specify the helper behavior and how it diagnoses batch layout.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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