r-bioinformatics/edgePy

data normalization functions

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#9 opened on May 16, 2018

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feature requesthelp wanted

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Description

Functions for normalizing read count data:

First:

(and other normalization methods)

  • TMM
  • RLE
  • UPPERQUANTILE

Contributor guide

Research direction
Implement FPKM normalization as shown in edgeR documentation, then proceed to TMM, RLE, and upper quantile normalization. Ensure consistency with existing CPM and RPKM implementations.
Tech stack
python
Domain
bioinformatics
Issue type
Feature
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
3
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-2 days
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
Pythonbiology fundamentals
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
50