https://github.com/ltla/pseudocount2018
Some thoughts on choosing an appropriate pseudo-count for log-transformation of scRNA-seq counts.
https://github.com/ltla/pseudocount2018
Last synced: 11 months ago
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Some thoughts on choosing an appropriate pseudo-count for log-transformation of scRNA-seq counts.
- Host: GitHub
- URL: https://github.com/ltla/pseudocount2018
- Owner: LTLA
- Created: 2018-07-15T16:39:58.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2018-11-19T10:39:44.000Z (over 7 years ago)
- Last Synced: 2025-06-24T07:04:56.588Z (12 months ago)
- Language: TeX
- Size: 71.3 KB
- Stars: 9
- Watchers: 3
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Errors upon log-transformation of scRNA-seq data
This repository contains code and manuscript files for the paper **Overcoming systematic errors caused by log-transformation of normalized single-cell RNA sequencing data**
by [Lun (2018)](https://doi.org/10.1101/404962).
The `report` subdirectory contains LaTeX files for the report.
The `scripts` subdirectory contains R code to reproduce the analyses described in the report:
- `spurious_sim.R`, to examine the non-zero log-fold change induced by the log-transformation.
- `substructure.R`, to examine the introduction of structural artifacts due the log-transformation.
- `alternatives.R`, to examine the performance of other transformations.
- `check_ercc.R`, to examine the behaviour of the log-transformation on real data.
- `power_sim.R`, to examine the consequences on detection power with an increased pseudo-count.