Magnushhoie / Biodatascience101_notebooks Public

Notifications You must be signed in to change notification settings
Fork 2
Star 5

Biological data-science Jupyter notebooks designed for biodatascience101.github.io

Notifications

Name		Name	Last commit message	Last commit date
Latest commit History 29 Commits
img		img
Module_1_Malaria_PandasIO_MH_AFM.ipynb		Module_1_Malaria_PandasIO_MH_AFM.ipynb
Module_2_Sequence_DataVisualization__public_MH_AFS.ipynb		Module_2_Sequence_DataVisualization__public_MH_AFS.ipynb
README.md		README.md

Repository files navigation

Datascience_teaching_notebooks

Collection of notebooks used for teaching data science, developed by Magnus Haraldson Høie and Andreas Fønss Møller

Module 1: Data Exploration - Biomarkers for cerebral Malaria in protein expression data

This module covers dataset I/O handling, modelling and normalisation in Pandas, principal component analysis and differential gene expression analysis. The case data is on quantification of relative protein levels in malaria-infected mice from work by Tiberti, N et al Scientific Reports 2016.

Module 2: Data Visualisation - Sequence features for thermostability in proteins from extremophiles

This module covers efficient data processing in Numpy, analysis and visualisation of biological sequences and graphing in Seaborn and Matplotlib. The case data comes from a dataset of 7.7 million bacterial sequences with associated temperature data compiled by the iGEM Potsdam team for Kaggle, collected from the Bacterial Diversity Metadatabase and UniProt.