Every 3 months we organise one day dedicated to the GTN community! Thursday, May 20th is the next GTN CoFest. We will be working on the training materials, have discussions with the global Galaxy traning community. Do you teach with Galaxy? Want to learn how to add your tutorial to the GTN? New to the community and just want to learn more? Everybody is welcome!
Full StoryMaria Doyle
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.
Editorial Roles
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.
Tutorials
- Assembly / Making sense of a newly assembled genome π§
- Assembly / De Bruijn Graph Assembly π§
- Assembly / An Introduction to Genome Assembly π§
- Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) π§
- Epigenetics / Identification of the binding sites of the Estrogen receptor π§
- Epigenetics / ATAC-Seq data analysis βοΈ
- Transcriptomics / Reference-based RNA-Seq data analysis βοΈ π§
- Transcriptomics / Visualization of RNA-Seq results with CummeRbund π§
- Transcriptomics / GO Enrichment Analysis βοΈ π§
- Transcriptomics / 2: RNA-seq counts to genes βοΈ π§
- Transcriptomics / 1: RNA-Seq reads to counts βοΈ π§
- Transcriptomics / Network analysis with Heinz π§
- Transcriptomics / Visualization of RNA-Seq results with Volcano Plot in R βοΈ
- Transcriptomics / Visualization of RNA-Seq results with heatmap2 βοΈ
- Transcriptomics / 3: RNA-seq genes to pathways βοΈ
- Transcriptomics / Visualization of RNA-Seq results with Volcano Plot βοΈ
- Introduction to Galaxy Analyses / From peaks to genes π§
- Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy π§
- Introduction to Galaxy Analyses / Galaxy Basics for genomics π§
- Introduction to Galaxy Analyses / A short introduction to Galaxy π§
- Variant Analysis / Microbial Variant Calling π§
- Variant Analysis / Calling very rare variants π§
- Using Galaxy and Managing your Data / Extracting Workflows from Histories π§
- Using Galaxy and Managing your Data / Using dataset collections π§
- Genome Annotation / CRISPR screen analysis βοΈ
- Genome Annotation / Genome annotation with Prokka π§
- Sequence analysis / Mapping π§
- Sequence analysis / Quality Control βοΈ π§
Slides
- Galaxy Server administration / Advanced customisation of a Galaxy instance π§
- Using Galaxy and Managing your Data / Getting data into Galaxy βοΈ
- Genome Annotation / Introduction to CRISPR screen analysis βοΈ
FAQs
Video Recordings
- Genome Annotation / Introduction to CRISPR screen analysis π¬
- Transcriptomics / Visualization of RNA-Seq results with Volcano Plot in R π¬ π£
- Transcriptomics / Visualization of RNA-Seq results with Volcano Plot π¬ π£
- Genome Annotation / CRISPR screen analysis π¬ π£
GitHub Activity
github Issues Reported
49 Merged Pull Requests
See all of the github Pull Requests and github Commits by Maria Doyle.
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Fix zenodo links
genome-annotation
- RNA-seq reads counts: small update
- Crispr slides fix
- CRISPR: Add speaker notes to slide
- CRISPR finalise
Reviewed 13 PRs
We love our community reviewing each other's work!
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Update Transcriptomics Reference-based tutorial
transcriptomicstemplate-and-tools
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Quality control: update tutorial to include FASTQE
CoFest
- Reconfiguration of some content in mouse RNA-seq tutorials
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Ref-based RNA-Seq: some fixes, reorganization, QC checks on mapped reads
transcriptomics
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RNA-seq limma-voom rework
transcriptomicsnew tutorial
News
Author(s) | Maria Doyle |
The Volcano plot tutorial introduced volcano plots and showed how they can be easily generated with the Galaxy Volcano plot tool. This new tutorial shows how you can customise a plot using the R script output from the tool and RStudio in Galaxy. A short video for the tutorial is also available on YouTube, created for the GCC2021 Training week. Happy plotting!
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