epam / epam/fonda

Create new sample mapping strategy for multiomics single cell

Open
#201 0 comments 0 reactions 0 assignees View on GitHub
enhancement
Dominant language
Java
Stars
8
Forks
2
PR merge metrics
No merged PRs in 30d

Description

# Issue

Currently, `1:M` sample mapping in single cell is solved by creating master (GEX) column for Antibody library type. This strategy creates line duplication and obliges the creation of the main columns manually.

# Approach

Create new sample mapping strategy by grouping:
- Create group membership:
- single mandatory field
- value: group membership or `NA/NULL`

- Group processing:
- split samples into groups
- duplicate `Antibody` sample type to create a `1:1` relationship for a group containing more than `1:1` mapping
- treat sample as singleton if group column is `NA` or `NULL`

Contributor guide

Open the contributing guide

Research direction

No files, tests, or entry points are named. Start by locating the existing single-cell 1:M sample-mapping logic and its tests, then trace how master GEX and Antibody columns are created. Done means grouped samples support mandatory membership values, singleton NA/NULL samples, and the described 1:1 Antibody mapping without manual master columns.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

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