This is an step-by-step on doing a gene regulatory analysis. Data used for this analysis are publicly available in Sequence Read Archive (SRA-NCBI), Gene Expression Omnibus (GEO-NCBI) or Array Express.
Links to data specified on the scripts:
For package installing, there is two sources: The Comprehensive R Archive Network - CRAN - and Bioconductor. To install CRAN packages, on the R console, just type:
install.packages("package")
For Bioconductor packages, the first installation requires the package BiocManager (from CRAN). After installing BiocManager, you can install Bioconductor packages using the following command on R console:
BiocManager::install("package")
The parameter package can be substituted by an character vector (c()) containing all packages to install.
R Packages used in this analysis:
- From CRAN
- BiocManager
- data.table
- classInt
- RColorBrewer
- ggplot2
- dplyr
- stringr
- FactoMineR
- Honorable Mention: tidyverse
- From Bioconductor
- affy
- limma
- biomaRt
- Fletcher2013b
- RTN
- RedeR
- enrichR
- edgeR
- DESeq2
Info: data.table, dplyr, and ggplot2 are part of the tidyverse. You are encouraged to install the entire plethora of packages from the Tidyverse and learn to work with them. They make R data analysis easier than it is with base.
More details will be added here.