e-learning
Scanpy Parameter Iterator
Abstract
The magic of bioinformatic analysis is that we use maths, statistics and complicated algorithms to deal with huge amounts of data to help us investigate biology. However, analysis is not always straightforward – each tool has various parameters to select. Eventually, we can end up with very different outcomes depending on the values we choose. With analysing scRNA-seq data, it’s almost like you need to know about 75% of your data, then make sure your analysis shows that, for you to then be able to identify the 25% new information.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How can I run a tool with multiple parameter values?
- Do I have to enter parameter values manually each time I want to check a new value?
- What tools can take multiple values at once and iterate over them?
Learning Objectives
- Execute the Scanpy Parameter Iterator
- Recognise what tools you can use Parameter Iterator with
- Operate tools working on dataset collections
- Compare plots resulting from different parameters values
Licence: Creative Commons Attribution 4.0 International
Keywords: Single Cell
Target audience: Students
Resource type: e-learning
Version: 7
Status: Active
Prerequisites:
- Combining single cell datasets after pre-processing
- Filter, plot and explore single-cell RNA-seq data with Scanpy
- Generating a single cell matrix using Alevin
- Introduction to Galaxy Analyses
Learning objectives:
- Execute the Scanpy Parameter Iterator
- Recognise what tools you can use Parameter Iterator with
- Operate tools working on dataset collections
- Compare plots resulting from different parameters values
Date modified: 2023-12-05
Date published: 2023-07-19
Contributors: Wendi Bacon
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