https://github.com/erictleung/bmi656-research-project
Final project for BMI 656 Bioinformatics Programming and Scripting
https://github.com/erictleung/bmi656-research-project
class-project h5n1 kegg-pathways odds-ratio project python python-programming
Last synced: 3 months ago
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Final project for BMI 656 Bioinformatics Programming and Scripting
- Host: GitHub
- URL: https://github.com/erictleung/bmi656-research-project
- Owner: erictleung
- Created: 2014-11-20T20:14:15.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2018-12-06T02:20:30.000Z (over 6 years ago)
- Last Synced: 2025-02-16T07:59:32.849Z (4 months ago)
- Topics: class-project, h5n1, kegg-pathways, odds-ratio, project, python, python-programming
- Language: Python
- Homepage:
- Size: 765 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
bmi656-research-project
=======================
This repository contains the files for the final project in BMI 656.
# odds.py
This script will perform an odds ratio calculation to identify pathways
containing a larger number of differentially expressed genes than would be
expected by chance.
This script will assume you have the following text files in the current
directory:
+ H5N1_VN1203_DE_Probes.txt
+ H5N1_VN1203_UNIVERSE_Probes.txt
+ KEGG_Pathway_Genes.txt
The script will parse through each of them and find KEGG pathways which have an
odds ratio greater than 1.5. A KEGG pathway will be chose out of the ones with
an odds ratio greater than 1.5 to study further in the next section.
# crossSpecies.py
# Deliverables
+ (60 points) Write Part I and Part II as separate python programs that are both called from a linux bash script. This script should check for the existence of relevant files and check that Part I has successfully completed before running Part II. Turn in both python programs and the bash script.
+ (10 points) Screen shot of pathway with highlighted differentially expressed genes
+ (10 points) Boxplot labeled with p-value of **Mann-Whitney statistic**
+ (20 points) 1-2 page write-up summarizing your findings. This should be a word document that includes at least 2
figures corresponding to your pathway and boxplot. Discuss the limitations of the study and any obstacles/problems you experienced. Discuss the relevance of the pathway to H5N1 infection. Discuss why the conservation of the affected pathway might be important for the study of H5N1 (Hint: think about our use of model organisms to study infectious diseases).