Maria 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.

• Topic: Transcriptomics

Tutorials

• Sequence analysis / Quality Control ✍️ 🧐
• Sequence analysis / Mapping 🧐
• Transcriptomics / GO Enrichment Analysis ✍️ 🧐
• Transcriptomics / Network analysis with Heinz 🧐
• Transcriptomics / 1: RNA-Seq reads to counts ✍️ 🧐
• Transcriptomics / Visualization of RNA-Seq results with CummeRbund 🧐
• Transcriptomics / Visualization of RNA-Seq results with Volcano Plot in R ✍️
• Transcriptomics / Visualization of RNA-Seq results with heatmap2 ✍️
• Transcriptomics / 3: RNA-seq genes to pathways ✍️
• Transcriptomics / 2: RNA-seq counts to genes ✍️ 🧐
• Transcriptomics / Visualization of RNA-Seq results with Volcano Plot ✍️
• Transcriptomics / Reference-based RNA-Seq data analysis ✍️ 🧐
• Genome Annotation / CRISPR screen analysis ✍️
• Genome Annotation / Genome annotation with Prokka 🧐
• Using Galaxy and Managing your Data / Using dataset collections 🧐
• Using Galaxy and Managing your Data / Extracting Workflows from Histories 🧐
• Assembly / Making sense of a newly assembled genome 🧐
• Assembly / An Introduction to Genome Assembly 🧐
• Assembly / De Bruijn Graph Assembly 🧐
• Introduction to Galaxy Analyses / From peaks to genes 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for genomics 🧐
• Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy 🧐
• Introduction to Galaxy Analyses / A short introduction to Galaxy 🧐
• Epigenetics / Identification of the binding sites of the Estrogen receptor 🧐
• Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) 🧐
• Epigenetics / ATAC-Seq data analysis ✍️
• Variant Analysis / Microbial Variant Calling 🧐
• Variant Analysis / Calling very rare variants 🧐

Slides

• Genome Annotation / Introduction to CRISPR screen analysis ✍️
• Using Galaxy and Managing your Data / Getting data into Galaxy ✍️
• Galaxy Server administration / Advanced customisation of a Galaxy instance 🧐

FAQs

• Importing via links
• Importing a workflow

Video Recordings

• Genome Annotation / Introduction to CRISPR screen analysis 💬
• Transcriptomics / Visualization of RNA-Seq results with Volcano Plot in R 💬 🗣
• Transcriptomics / Visualization of RNA-Seq results with Volcano Plot 💬 🗣
• Genome Annotation / CRISPR screen analysis 💬 🗣

Events

• Bioconductor Carpentries workshop: Analysis and Interpretation of Bulk RNA-Seq Data 🎪
• Bioconductor North American conference (BioC2024) 🎪
• EuroBioC2024 Carpentries workshops 🎪

GitHub Activity

github Issues Reported

49 Merged Pull Requests

See all of the github Pull Requests and github Commits by Maria Doyle.

• 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!

• Update Transcriptomics Reference-based tutorial
  transcriptomics
  template-and-tools
• Quality control: update tutorial to include FASTQE
  CoFest
• Reconfiguration of some content in mouse RNA-seq tutorials
• Ref-based RNA-Seq: some fixes, reorganization, QC checks on mapped reads
  transcriptomics
• RNA-seq limma-voom rework
  transcriptomics
  new tutorial

News

External Links

Favourite Topics

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