# Bioinformatics -Level1-Module 7-Maryam

**URL:** <http://staging.stemaway.com/t/bioinformatics-level1-module-7-maryam/9241>\
**Category:** R Shiny Transcriptomics App 2021\
**Created:** [August 25, 2021, 2:20pm UTC](http://staging.stemaway.com/t/bioinformatics-level1-module-7-maryam/9241 "2021-08-25T14:20:44Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Maryam](https://d3rzmptxz7fqzy.cloudfront.net/user_avatar/staging.stemaway.com/maryam/32/4491_2.png) [@Maryam](http://staging.stemaway.com/u/Maryam)\
**Post date:** [August 25, 2021, 2:20pm UTC](http://staging.stemaway.com/t/bioinformatics-level1-module-7-maryam/9241/1 "2021-08-25T14:20:44Z")

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**Module 7:‎ (Capstone project)**

**Technical Area**

• Reading datasets and meta-data in R

• Quality control

• Normalization and background correction

• Batch effect removal

• Annotation and gene filteration

• KEGG pathway and GO analysis

• GSEA

• Gene concept network analysis

• TFs analysis

• PPI network analysis by Cytoscape

• Survival analysis

**‎ Tools**

• R packages: Affy, arrayQualityMetrics , sva, ggplot2, pheatmap, WGCNA, limma, ‎EnhancedVolcano, hgu133plus2.db, enrichplot, org.Hs.eg.db, msigdbr, magrittr, ‎clusterProfiler, enrichplot, tidyr, clusterProfiler, Rcpp

• Cytoscape (STRING and Cytohubba plugins)‎

• GEPIA

**Soft Skills**

• I prepared a presentation of my Capstone project. So I worked on my presentation ‎skills

• Preparing Powerpoint for the presentation

**Tasks completed**

I merged two datasets containing 70 samples of lung cancer and removed the batch effect ‎between them and then implemented differential expression analysis for them. After ‎obtaining DEGs, I found enriched KEGG pathways and GO enriched terms for them. Then, I ‎plotted a gene-concept network and TF network for them and performed a GSEA. To find ‎hub genes I plotted a PPI network and found the 10 key genes in that network. After that, I ‎implemented the survival analysis for those 10 genes and found 5 genes that the value of ‎their expression was effective in the survival of patients with lung cancer.‎