Skip to content

raffael-azevedo/gene-regulatory-networks

Repository files navigation

Gene Regulatory Networks Generation using RTN R/Bioconductor package.

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:

  1. From CRAN
  • BiocManager
  • data.table
  • classInt
  • RColorBrewer
  • ggplot2
  • dplyr
  • stringr
  • FactoMineR
  • Honorable Mention: tidyverse
  1. 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.

About

No description, website, or topics provided.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages