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matteopilz committed Nov 20, 2024
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10 changes: 3 additions & 7 deletions docs/getting-started/knime-get-started.md
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KNIME
=====

## Installation
Click [here](knime/knime-installation.md) to install KNIME, the OpenMS plugin and its required packages.

## Ready-made KNIME workflows

You can get ready-made KNIME workflows and workflow components with OpenMS nodes from our
Expand All @@ -13,10 +10,10 @@ For more, e.g., thirdparty OpenMS workflows use the search bar on the hub and se
["openms"](https://hub.knime.com/search?q=openms).


## Creating workflows with KNIME
## Installing KNIME and creating workflows

Download Introduction to OpenMS in KNIME [user tutorial](/tutorials/knime-user-tutorial.md) containing hands-on training material covering also basic
usage of KNIME. See the official [KNIME Getting Started Guide](https://www.knime.com/getting-started-guide) for a more in-depth view of
Read through a introduction to OpenMS in KNIME [user tutorial](/tutorials/knime-user-tutorial.md) containing hands-on training material covering also basic
usage of KNIME and how to install it. See the official [KNIME Getting Started Guide](https://www.knime.com/getting-started-guide) for a more in-depth view of
the KNIME functionality besides OpenMS.

If you face any issues, please [contact us](/about/communication.md) and specifically for the usage of OpenMS in KNIME, the KNIME community contribution [forum](https://forum.knime.com/tag/openms).
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hidden: True
---
Install <knime/knime-installation.md>
knime/minimal-workflow.md
```
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3 changes: 1 addition & 2 deletions docs/manual/additional/swathwizard.md
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Expand Up @@ -3,8 +3,7 @@ SwathWizard

SwathWizard is an assistant for Swath analysis.

The Wizard takes the user through the whole analysis pipeline for SWATH proteomics data analysis, i.e. the
[TOPP Documentation: OpenSwathWorkflow](https://openms.readthedocs.io/en/latest/tutorials-and-quickstart-guides/openms-user-tutorial.html#id44) tool, including downstream tools such as [GitHub:PyProphet/pyProphet](https://github.com/PyProphet/pyprophet) and the [GitHub:msproteomicstools/TRIC alignment](https://github.com/msproteomicstools/msproteomicstools) tool.
The Wizard takes the user through the whole analysis pipeline for SWATH proteomics data analysis, including downstream tools such as [GitHub:PyProphet/pyProphet](https://github.com/PyProphet/pyprophet) and the [GitHub:msproteomicstools/TRIC alignment](https://github.com/msproteomicstools/msproteomicstools) tool.

Since the downstream tools require Python and the respective modules, the Wizard will check their proper installation
status and warn the user if a component is missing.
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