Mehmet Tekman

Affiliations

University of Freiburg avatar UFR🖖🏾Single-cell & sPatial Omics Community of practice avatar 🖖🏾SPOC

Former Affiliations

ELIXIR Europe avatar ELIXIR Europe

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

1 Editorial Role

This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.

54 Tutorials

17 Slides

15 FAQs

6 Video Recordings



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Mehmet Tekman avatar
Mehmet Tekman

54 Tutorials 17 Slides 15 FAQs 8 News 6 Videos Editorial Board

GTN contributor since 2018-11

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GitHub Activity

Issues Reported

57 Merged Pull Requests

See all of the Pull Requests and Commits by Mehmet Tekman.

Reviewed 41 PRs

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News

Arabidopsis clusters with trajectory from meristematic cells towards trichoblasts
New Tutorial: Downstream Single-cell RNA Plant analysis with ScanPy
Mehmet Tekman avatar Beatriz Serrano-Solano avatar
30 March 2021
Single cell RNA-seq analysis is a cornerstone of developmental research and provides a great level of detail in understanding the underlying dynamic processes within tissues. In the context of plants, this highlights some of the key differentiation pathways that root cells undergo.
new tutorial single-cell plant
Pretty dots of different colours combined into two cell cluster plots on the sides. In the middle, a split violin plot showing the expression of unknown genes in blue on one side and the expression of the genes in an opposing sample in orange alongside. Snuck in between these three important plots is a PhD comic of data showing no trend, with the chat box “Hmm… I think there’s a clear trend happening here.”
New Topic: Single Cell Analysis!
Wendi Bacon avatar Mehmet Tekman avatar
18 November 2022
Single-cell analysis now has it’s own topic! These tutorials were previously part of the transcriptomics topic, but due to the amazing efforts by Wendi Bacon, Mehmet Tekmanand others, we now have so many single-cell analysis tutorials that they deserve their own dedicated topic! From introductory slides and practicals, to case study tutorials generating cell clusters and trajectories from raw sequencing files, and even a growing subtopic of smaller tips and tricks for adapting analysis to user needs, the single cell topic either has what you need or is working on it. Come learn or get involved!
new topic single-cell new feature
Heatmap with columns of cell types vs rows of inferred and actual cell type proportions for A and B samples. Cell colours are similar between actual and inferred.
New Tutorial Suite: Deconvolution with MuSiC, from public data to disease interrogation!
Mehmet Tekman avatar Wendi Bacon avatar
29 November 2022
The still new and shiny single-cell analysis topic now boasts a deconvolution tutorial suite! What does deconvolution do you ask? Well, in this context, it infers cell proportions from bulk RNA-seq data. You heard that correctly - instead of expensive new single-cell experiments, you can re-analyse old bulk RNA-seq data and estimate cell proportions. All you need is a reasonably good single cell dataset to use as a reference and you’re good to go! The tutorial suite shows you how to build your reference from publicly available single cell data, and apply analysis to some publicly available bulk RNA-seq data.
new tutorial single-cell transcriptomics
GTN logo with a multi-coloured star and the words Galaxy Training Network
GTN Helper Bots Connect the Galaxy
Mehmet Tekman avatar
20 December 2023
🤖💬 Bleep bloop! Good news everyone! We have deployed some bots to enable our Matrix regulars to better engage with the contributions and questions of our users on the non-Matrix side of the Galaxy-verse.
gtn communications contributing
GTN logo with a multi-coloured star and the words Galaxy Training Network
GTN Helper Bots Connect the Galaxy
Mehmet Tekman avatar
20 December 2023
🤖💬 Bleep bloop! Good news everyone! We have deployed some bots to enable our Matrix regulars to better engage with the contributions and questions of our users on the non-Matrix side of the Galaxy-verse.
gtn communications contributing
swirled cluster dots surround a circle of people all holding hands, looking towards the bright center (future)
Galaxy Single-cell Community: Year in Review
Mehmet Tekman avatar Wendi Bacon avatar Pavankumar Videm avatar
22 December 2023
🚀Embarking on a cosmic journey, the Galaxy Single-cell Community has clustered together to unveil a constellation of tools, making strides in RNA-stellar discoveries and creating out-of-this-world workflows. With a commitment to battling work duplication across the multiverse, this community is boldly charting a course for global domination, proving that when it comes to bioinformatics, the Galaxy is the limit!✨
gtn communications single-cell
cropped picture of a mobile phone interface showing a terminal with Galaxy log outputs.
🪐📲 Hosting Galaxy at the Edge: Directly in Your Pocket!
Mehmet Tekman avatar
31 January 2024
Hey Galaxy admins! Have you ever wanted to administer your own instance from the luxury of your pocket?
fun system administrators developers humour admin
cropped picture of a mobile phone interface showing a terminal with Galaxy log outputs.
🪐📲 Hosting Galaxy at the Edge: Directly in Your Pocket!
Mehmet Tekman avatar
31 January 2024
Hey Galaxy admins! Have you ever wanted to administer your own instance from the luxury of your pocket?
fun system administrators developers humour admin
Mehmet Tekman avatar
GTN contributor since 2018-11

External Links

mtekman
mtekman89@gmail.com
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