This repository aims to share the codes developed for the analysis of differential expression of transcripts using data from RNA-seq. The input data, such as counts, metadata, and fpkm values, can be downloaded from the Zenodo repository (https://doi.org/10.5281/zenodo.8216030).
The Dockerfile presented in the docs directory is a Docker file used to create an RStudio image with all the necessary packages to run the scripts.
The parcial_report directory includes the scripts written for the partial project report. It complements the pipeline_deseq2 file, which performs differential expression analysis between groups, constructs Venn diagrams and heatmaps for the DESeq2 program. The same applies to the pipeline_edger file, but for the edgeR program. The pipeline_fpkm file performs variance analyses between FPKM values of genes and their samples related to renal carcinoma data.
The remaining directories (005_preqc to 205_gwena) contains the necessary scripts for sample pre-processing, differential expression analysis, network analysis, and functional annotation. Access the tutorial at https://rpubs.com/jpietro/vignette_pipeline for a step by step guide through the pipeline.