index-plants.md

layout	website	subdomain	gitter
subsite-galaxy	https://plants.usegalaxy.eu	plants	usegalaxy-eu/Lobby

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Welcome to Galaxy for Plant Biology

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The Plant Anaylsis Workbench is a comprehensive set of analysis tools and consolidated workflows. The workbench is based on the Galaxy framework{:target="_blank"}, which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge.

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Get started

Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take a [guided tour]({{ page.website }}/tours/core.galaxy_ui){:target="_blank"} through Galaxy's user interface.

Training

We are working in close collaboration with the Galaxy Training Network (GTN){:target="_blank"} to develop training materials of data analyses based on Galaxy. If you want to know more about the GTN or how to become part of the Galaxy community, check the videos below!

<iframe width="560" height="315" src="https://www.youtube.com/embed/lDqWxzWNk1k" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen> </iframe> <iframe width="560" height="315" src="https://www.youtube.com/embed/-1MPdxmRs8U" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

Workshops

• Plant Transcriptome Analysis Workshop, April 19-23, 2021.

Training material

All relevant materials for plant-related data analysis can also be found within the GTN.

Lesson	Slides	Hands-on	Input dataset	Workflows	Galaxy History
Welcome and introduction to Galaxy	{:target="_blank"} / {:target="_blank"}
An Introduction to Transcriptomics	{:target="_blank"} / {:target="_blank"}
Quality Control	{:target="_blank"} / {:target="_blank"}	{:target="_blank"} / {:target="_blank"}	{:target="_blank"}	{:target="_blank"}	[]({{ page.website }}/u/gallardoalba/h/quality-control){:target="_blank"}
Mapping	{:target="_blank"} / {:target="_blank"}	{:target="_blank"} / {:target="_blank"}	{:target="_blank"}	{:target="_blank"}	[]({{ page.website }}/u/gallardoalba/h/mapping){:target="_blank"}
miRNA data analysis	{:target="_blank"} / {:target="_blank"}	{:target="_blank"} / {:target="_blank"}	{:target="_blank"}	{:target="_blank"}	[]({{ page.website }}/u/gallardoalba/h/mirna-data-analysis){:target="_blank"}
mRNA data analysis and miRNA target prediction		{:target="_blank"} / {:target="_blank"}	{:target="_blank"}	{:target="_blank"}	[]({{ page.website }}/u/videmp/h/arabidopsis-transcriptome-analysis){:target="_blank"}
An introduction to single-cell RNA-seq data analysis	{:target="_blank"} / {:target="_blank"}
Understanding Barcodes	{:target="_blank"} / {:target="_blank"}	{:target="_blank"} / {:target="_blank"}	{:target="_blank"}	[]({{ page.website }}/workflows/run?id=d7aa4c258e2edc95){:target="_blank"}	[]({{ page.website }}/u/mehmet-tekman/h/understanding-barcodes){:target="_blank"}
Pre-processing of 10X Single-Cell RNA Datasets		{:target="_blank"} / {:target="_blank"}	{:target="_blank"}	[]({{ page.website }}/workflows/run?id=d79309343e2a5d62){:target="_blank"}	[]({{ page.website }}/u/mehmet-tekman/h/pre-processing-of-10x-single-cell-rna-star-278a){:target="_blank"}
Clustering 3K PBMCs with ScanPy	{:target="_blank"}	{:target="_blank"} / {:target="_blank"}	{:target="_blank"}	[]({{ page.website }}/workflows/run?id=921cab3e6faf30be){:target="_blank"}	[]({{ page.website }}/u/mehmet-tekman/h/clustering-3k-pbmcs-with-scanpy){:target="_blank"}
Analysis of plant scRNA-Seq data using ScanPy		{:target="_blank"} / {:target="_blank"}	{:target="_blank"}	[]({{ page.website }}/workflows/run?id=d70dc4cfeedb690b){:target="_blank"}	[]({{ page.website }}/u/mehmet-tekman/h/analysis-of-plant-scrna-seq-data-with-scanpy){:target="_blank"}
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Partners

This service is a joint project between different groups from the DataPLANT Consortium{:target="_blank"}, the BioDATEN project{:target="_blank"}, VIB{:target="_blank"}, IPK{:target="_blank"}, and the University of Freiburg{:target="_blank"}. The service is part of the European Galaxy server and is maintained by the RNA Bioinformatics Center (RBC){:target="_blank"} as part of de.NBI{:target="_blank"} and ELIXIR{:target="_blank"}.