https://github.com/arkanivasarkar/rnaseq-data-analysis-pipeline

Pipeline for analyzing RNAseq data of human and mouse - beginner friendly with minimal user inputs
https://github.com/arkanivasarkar/rnaseq-data-analysis-pipeline

bioinformatics differential-gene-expression rna-seq rna-seq-pipeline

Last synced: 2 months ago
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Pipeline for analyzing RNAseq data of human and mouse - beginner friendly with minimal user inputs

• Host: GitHub
• URL: https://github.com/arkanivasarkar/rnaseq-data-analysis-pipeline
• Owner: arkanivasarkar
• Created: 2021-08-30T16:23:41.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2021-08-30T18:35:20.000Z (over 3 years ago)
• Last Synced: 2025-02-01T21:32:20.428Z (4 months ago)
• Topics: bioinformatics, differential-gene-expression, rna-seq, rna-seq-pipeline
• Language: R
• Homepage:
• Size: 1.52 MB
• Stars: 0
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# RNAseq Data Analysis Pipeline

This repository contains the workflow of RNAseq data analysis.

This pipeline performs the following tasks:

- Reading data

- align reads of each sample in a run against reference genome

= perform quality control on generated BAM files 

- count reads in features 

- normalize read counts

- Filtering lowly expressed genes

- perform DE analysis 

## Dataset

The data used for analysis is from the study, “EGF-mediated induction of Mcl-1 at the switch to lactation is essential for alveolar cell survival” (Fu et al. 2015).

This study examines the expression profiles of basal stem-cell enriched cells  and committed luminal cells in the mammary gland of virgin, pregnant and lactating mice.

GEO Accession ID - [GSE60450](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60450)

The read count data, metadata and the fastq files are present in `Datasets` folder.

## Results

The differentially expressed genes were obtained. 

Various plots like heatmap, mean-variance plot, MA plot, and volcano plot were made to analyse the data better.

### Library Size of the Samples

[![Picture4.png](https://i.postimg.cc/DykqwfhK/Picture4.png)](https://postimg.cc/0rn6tsrt)

### HeatMap

[![Picture3.png](https://i.postimg.cc/v8zQc3FH/Picture3.png)](https://postimg.cc/w31Kr5jS)

### Mean-Variance Plot

[![Picture1.png](https://i.postimg.cc/50QCfTk0/Picture1.png)](https://postimg.cc/ygBdPQK4)

### MA Plot & Volcano Plot

[![Picture2.png](https://i.postimg.cc/LXFHZW8h/Picture2.png)](https://postimg.cc/7CXvFm7y)