https://github.com/ltla/counterspell2018
UU: Counter target spell.
https://github.com/ltla/counterspell2018
Last synced: 4 months ago
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UU: Counter target spell.
- Host: GitHub
- URL: https://github.com/ltla/counterspell2018
- Owner: LTLA
- Created: 2018-07-11T08:48:20.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2018-10-16T04:05:54.000Z (over 7 years ago)
- Last Synced: 2025-02-10T12:29:09.524Z (over 1 year ago)
- Language: TeX
- Homepage:
- Size: 42 KB
- Stars: 8
- Watchers: 3
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Criticisms of MAGIC in scRNA-seq data
This repository contains code to explore some of the consequences of using MAGIC in scRNA-seq data.
The `report` subdirectory contains LaTeX files for the report, which you can compile yourself if you know how.
The `scripts` subdirectory contains R code to reproduce the analyses described in the report:
- `nostruct_sim.R`, to examine the effect of using MAGIC in a simulation without any structure.
- `structloss_sim.R`, involving a simulation containing primary and secondary separations.
- `fakede_sim.R`, involving DE analysis between two well-separated subpopulations.
- `run_ercc.R`, to examine the effect of using MAGIC on the ERCC data set from 10X Genomics.
- `run_293t.R`, to examine the effect of using MAGIC on the 293T data set from 10X Genomics.
- `run_tb.R`, to test behaviour when combining B and T cells.