Anton Nekrutenko

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.

• Assembly
• Variant Analysis
• Introduction to Data Driven Life Sciences

Tutorials

• Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS 🧐
• Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step ✍️ 🧐
• Assembly / Making sense of a newly assembled genome ✍️ 🧐
• Assembly / Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data ✍️ 🧐
• Assembly / Unicycler Assembly ✍️ 🧐
• Transcriptomics / Reference-based RNAseq data analysis (long) ✍️
• Introduction to Galaxy Analyses / NGS data logistics ✍️ 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for genomics ✍️ 🧐
• Introduction to Galaxy Analyses / Very Short Introductions: QC ✍️ 🧐
• Introduction to Galaxy Analyses / IGV Introduction ✍️
• Variant Analysis / Pox virus genome analysis from tiled-amplicon sequencing data 🧐
• Variant Analysis / Calling variants in diploid systems ✍️
• Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis ✍️ 🧐
• Variant Analysis / Avian influenza viral strain analysis from gene segment sequencing data 🧐
• Variant Analysis / Calling variants in non-diploid systems ✍️ 🧐
• Variant Analysis / Calling very rare variants ✍️
• Using Galaxy and Managing your Data / Understanding Galaxy history system ✍️ 🧐
• Using Galaxy and Managing your Data / Using dataset collections ✍️ 🧐
• Using Galaxy and Managing your Data / Searching Your History ✍️
• Using Galaxy and Managing your Data / Multisample Analysis ✍️
• Genome Annotation / Comparative gene analysis in unannotated genomes ✍️ 🧐
• Foundations of Data Science / Versioning your code and data with git ✍️
• Foundations of Data Science / Introduction to sequencing with Python (part two) ✍️
• Foundations of Data Science / Introduction to sequencing with Python (part three) ✍️
• Foundations of Data Science / Introduction to sequencing with Python (part four) ✍️
• Foundations of Data Science / Introduction to sequencing with Python (part one) ✍️
• Foundations of Data Science / Data manipulation with Pandas ✍️
• Foundations of Data Science / A (very) brief history of genomics ✍️ 🧐

Slides

• Assembly / Unicycler Assembly ✍️ 🧐
• Assembly / Deeper look into Genome Assembly algorithms ✍️
• Foundations of Data Science / A brief history of modern biology ✍️ 🧐

FAQs

• How to enable the Activity Bar
• Upload fasta datasets via links
• Upload fastqsanger datasets via links
• Adding a tag
• Changing the datatype
• Changing database/build (dbkey)
• How to delete datasets?
• How to hide datasets?
• Importing via links
• Manipulating multiple history datasets
• How to un-delete datasets?
• How to un-hide datasets?
• Upload datasets from GenomeArk
• History annotation
• Creating a new history
• Dataset colors
• Dataset snippet
• Datasets versus collections
• View a list of all histories
• History options
• Renaming a history
• View histories side-by-side
• Switching to an existing history
• History tagging
• Top level history controls
• Undeleting history
• Why does the query `SRR11772204 OR SRR11597145 OR SRR11667145` in the Run Selector not return any results?
• Import workflows from DockStore
• Import workflows from WorkflowHub

Video Recordings

• Introduction to Galaxy Analyses / NGS data logistics 💬 🗣
• Introduction to Galaxy Analyses / Galaxy Basics for genomics 🗣
• Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis 💬 🗣
• Using Galaxy and Managing your Data / Using dataset collections 🗣

Events

• Galaxy Training Academy 2024 🎪

GitHub Activity

github Issues Reported

40 Merged Pull Requests

See all of the github Pull Requests and github Commits by Anton Nekrutenko.

• History tutorial update
  template-and-tools
  galaxy-interface
  faqs
• Very short introductions: QC
  introduction
• modernization of Galaxy101
  introduction
  template-and-tools
  faqs
• Gnmx l7
  data-science
• Update tutorial.md
  data-science

Reviewed 17 PRs

We love our community reviewing each other's work!

• History tutorial update
  template-and-tools
  galaxy-interface
  faqs
• Very short introductions: QC
  introduction
• modernization of Galaxy101
  introduction
  template-and-tools
  faqs
• Simplify MSA generation steps in tutorials by using latest MAFFT version
  variant-analysis
• Long vgp tutorial edits
  assembly

External Links

Favourite Topics

Favourite Formats