https://github.com/mouzkolit/neurobeginner
Data Science Beginner Course teached Jan 23
https://github.com/mouzkolit/neurobeginner
data-science matplotlib pandas python scanpy scrna-seq
Last synced: about 2 months ago
JSON representation
Data Science Beginner Course teached Jan 23
- Host: GitHub
- URL: https://github.com/mouzkolit/neurobeginner
- Owner: mouzkolit
- Created: 2023-01-17T21:00:19.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2023-04-07T20:29:23.000Z (about 3 years ago)
- Last Synced: 2025-03-11T08:34:36.642Z (over 1 year ago)
- Topics: data-science, matplotlib, pandas, python, scanpy, scrna-seq
- Language: Jupyter Notebook
- Homepage:
- Size: 47.3 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
Neuroscience Data Analysis Beginner Course
The following Content is provided for Neuroscientist to get a general overview
about Data-Science and Exploratory Data Analysis using the Python Language from the Medical Univeristy of Innsbruck
The Course is offered in the winter semester, and is conducted by Maximilian Zeidler, Kai Kummer und David Zimmermann
This course has the following Topics:
- Data Files are located in the Data Folder
- Tabular Data
- Parkinson DataSets
- IV Dataset (iv_condition.csv)
- Calcium Imaging Dataset
- Natural Language Processing
- Signal Processing
- Single Cell Sequencing/Bulk RNA Sequencing
- Analysis Script for the Data
- Basic Python
- Basic Matplotlib
- Basic Pandas/Numpy
- Basic Clustering
- Basic Dimensional Reduction
- Basic Pandas: Pubmed Analysis
- Basic Tabular: Parkinson Analysis
- Basic Calcium: Calcium Imaging Data Loading
- Single Cell Sequencing Analysis
- Basic PatchClamp: Patch-Clamp Analysis of preprocessed IV Traces
- Games and Fun
- First download and install miniconda, add it to your path variable (selecting the checkbox
- Open command line in Windows
- Type conda to see if everything is functional
You will get an overview about different data types retrieved from next-generation sequencing, electrophysiological measurements (Fura Data, Patch-Clamp)
and also from tabular data representing parkinson data and diabetis data which enables us to perform certain predictions
How to set up a virtual enviroment using conda
The execute the following:
```
# create a new enviroment
conda create -n neurobeginner
conda activate neurobeginner
# check if neurobeginner is at the beginning of your line in the terminal/cmd
conda install -c anaconda ipykernel
python -m ipykernel install --user --name=neurobeginner
conda install pandas
conda install seaborn
conda install matplotlib
```
Open then Powershell and download the latest file for the scRNA sequencing analysis
```
Invoke-WebRequest https://raw.githubusercontent.com/mouzkolit/NeuroBeginner/main/Scripts/instrcuted_single_cell_analysis.ipynb -OutFile scRNA.ipynb
```