https://github.com/saezlab/process_rnaseq_cellines

Processing RNAseq data from Cell Lines. From raw data to normalised, voom and ComBat batch-correction
https://github.com/saezlab/process_rnaseq_cellines

Last synced: 21 days ago
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Processing RNAseq data from Cell Lines. From raw data to normalised, voom and ComBat batch-correction

• Host: GitHub
• URL: https://github.com/saezlab/process_rnaseq_cellines
• Owner: saezlab
• License: gpl-3.0
• Created: 2019-07-31T15:04:15.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2020-11-11T12:38:10.000Z (over 5 years ago)
• Last Synced: 2025-01-22T07:37:40.549Z (over 1 year ago)
• Language: R
• Size: 2.46 MB
• Stars: 2
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# process_rnaseq_cellines

Processing RNAseq data from Cell Lines. The process_rnaseq_cellines_* files

are pipelines that follow the next steps:

 - Imputes 0 to NA values

 - Removes samples exeding genes with 0

 - Removes non-expressed genes with average CPM <=0

 - Normalises through TMM method

 - Runs Voom transformation

 - Uses ComBat for Batch correction of voom transformed data 

 - Merges duplicates by the mean

In the wiki of this repo the exploratory analysis of the data can be found.

# Technical details

R version 3.6.0 (2019-04-26)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: macOS Mojave 10.14.5

Packages:

- data.table 1.12.2

- dplyr 0.8.1

- stringr 1.4.0

- limma 3.40.2

- sva 3.32.1

- edgeR 3.26.4

- ggplot2 3.1.1

- ggforce 0.2.2

- ggfortify 0.4.7