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.
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