AlexsLemonade/training-modules

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• scRNA-seq-advanced: investigate changes for harmony 2

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  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  AlexsLemonade/training-modules#1095 · 2 comments · Opened Sep 29, 2026

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• Add C8 to notebooks that introduce msigbdr

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  Difficulty 2/5 1-3 hours Newbie friendliness 70/100

  AlexsLemonade/training-modules#1016 · Opened Jun 11, 2026

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• Swap size -> linewidth

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  Difficulty 2/5 1-3 hours Newbie friendliness 72/100

  AlexsLemonade/training-modules#1015 · Opened Jun 10, 2026

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• Write slides for spatial workshop

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  Epic

  Difficulty 5/5 Over a week Newbie friendliness 38/100

  AlexsLemonade/training-modules#1014 · Opened Jun 8, 2026

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• 2026 Intro scRNA-seq workshop fixes

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  Difficulty 1/5 Under an hour Newbie friendliness 72/100

  AlexsLemonade/training-modules#997 · 3 comments · Opened May 13, 2026

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• Potentially update GSEA notebook gmt file handling

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  Difficulty 3/5 1-2 days Newbie friendliness 55/100

  AlexsLemonade/training-modules#991 · Opened May 7, 2026

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• Expand data maintenance documentation

  May be free again @allyhawkins claimed this 44 days ago, and no pull request is open. Open

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  AlexsLemonade/training-modules#973 · 2 comments · 1 assignee · Opened Apr 17, 2026

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• Update external workshop instructions for new server

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  Difficulty 2/5 1-3 hours Newbie friendliness 64/100

  AlexsLemonade/training-modules#970 · Opened Apr 17, 2026

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• Update spatial cheatsheet links to point to rdrr

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  Difficulty 2/5 1-3 hours Newbie friendliness 64/100

  AlexsLemonade/training-modules#963 · Opened Apr 13, 2026

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• Update how we install Python packages in Docker

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  AlexsLemonade/training-modules#885 · Opened Jan 21, 2026

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• Ignore data files for gitignore.user

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  Difficulty 3/5 1-2 days Newbie friendliness 35/100

  AlexsLemonade/training-modules#799 · 1 comment · Opened Aug 21, 2024

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• Consider changing default branch to `main`

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  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  AlexsLemonade/training-modules#750 · Opened Aug 25, 2023

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• What is the future of rdrr?

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  Difficulty 5/5 Over a week Newbie friendliness 20/100

  AlexsLemonade/training-modules#706 · 3 comments · Opened Apr 13, 2023

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• Cheatsheets reorganized by topic

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  nice to have

  Difficulty 5/5 Over a week Newbie friendliness 25/100

  AlexsLemonade/training-modules#683 · Opened Mar 23, 2023

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• Nice to have for scAdvanced: resource document covering differential cell type abundance

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  AlexsLemonade/training-modules#604 · 1 comment · Opened Jan 3, 2023

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• Consider a separate directory for reference files

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  Difficulty 4/5 3-5 days Newbie friendliness 30/100

  AlexsLemonade/training-modules#557 · 1 comment · Opened Sep 23, 2022

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• Update links in RNA-seq, pathway-analysis, and machine-learning cheatsheets

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  Difficulty 2/5 Half a day Newbie friendliness 55/100

  AlexsLemonade/training-modules#528 · 1 comment · Opened Mar 3, 2022

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• Add rendering of module cheatsheets to make-live workflow

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  Difficulty 3/5 1-2 days Newbie friendliness 48/100

  AlexsLemonade/training-modules#523 · Opened Feb 28, 2022

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• DESeqDatasetFromMatrix() doesn’t like tibbles?

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  Difficulty 2/5 1-3 hours Newbie friendliness 45/100

  AlexsLemonade/training-modules#448 · 1 comment · Opened Mar 26, 2021

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• Fix rendering of character vectors

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  Difficulty 4/5 3-5 days Newbie friendliness 25/100

  AlexsLemonade/training-modules#443 · 2 comments · Opened Mar 15, 2021

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• Decide on consistent terms in intro to R: environment/workspace

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  Difficulty 3/5 1-2 days Newbie friendliness 35/100

  AlexsLemonade/training-modules#413 · Opened Mar 3, 2021

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• Add exercise notebook dev to contributing

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  contributing

  Difficulty 1/5 1-3 hours Newbie friendliness 55/100

  AlexsLemonade/training-modules#396 · 1 reaction · Opened Feb 28, 2021

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• Add option in `make-live.R` to only render

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  Difficulty 2/5 1-3 hours Newbie friendliness 45/100

  AlexsLemonade/training-modules#389 · 1 comment · Opened Feb 25, 2021

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• Set width parameter for consistent rendering

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  Difficulty 3/5 1-2 days Newbie friendliness 35/100

  AlexsLemonade/training-modules#370 · Opened Feb 22, 2021

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• Run two gastric samples for bulk RNA-seq

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  AlexsLemonade/training-modules#368 · 3 comments · Opened Feb 22, 2021

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• GHA: Submit a PR with rendered and live versions of notebook upon merge to master

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  automate all the things

  Difficulty 4/5 3-5 days Newbie friendliness 25/100

  AlexsLemonade/training-modules#359 · 3 comments · Opened Feb 20, 2021

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• Contributing guidelines for adding input files to /shared

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  contributing

  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  AlexsLemonade/training-modules#357 · Opened Feb 20, 2021

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• CONTRIBUTING: Guidelines for numbering and naming notebooks

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  contributing

  Difficulty 2/5 1-3 hours Newbie friendliness 55/100

  AlexsLemonade/training-modules#352 · Opened Feb 19, 2021

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• Update directory layout in scRNA-seq modules

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  Difficulty 2/5 1-3 hours Newbie friendliness 42/100

  AlexsLemonade/training-modules#341 · Opened Feb 17, 2021

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• Revisit setting repos in `.Rprofile` once we have more information about server installation

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  Difficulty 5/5 Over a week Newbie friendliness 20/100

  AlexsLemonade/training-modules#308 · Opened Feb 2, 2021

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• [Idea] What's a gene identifier anyway? Add resources for people with this question

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  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  AlexsLemonade/training-modules#288 · Opened Jul 30, 2020

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• What is dimension reduction anyway?

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  Difficulty 4/5 3-5 days Newbie friendliness 38/100

  AlexsLemonade/training-modules#286 · Opened Jul 29, 2020

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• include doublet detection in scRNA-seq

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  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  AlexsLemonade/training-modules#285 · 1 reaction · Opened Jul 29, 2020

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• Update tag-based workflow diagrams to include tximport

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  Difficulty 3/5 Half a day Newbie friendliness 45/100

  AlexsLemonade/training-modules#284 · Opened Jul 27, 2020

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• Talk about scRNA-seq memory usage and rm()

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  Difficulty 2/5 1-3 hours Newbie friendliness 45/100

  AlexsLemonade/training-modules#250 · 1 comment · Opened Jul 13, 2020

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• Discussion: Directory structure for modules on server

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  discussion

  Difficulty 5/5 Over a week Newbie friendliness 20/100

  AlexsLemonade/training-modules#246 · 5 comments · Opened Jul 8, 2020

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• Suggestion from participant: Show directory structure more

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  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  AlexsLemonade/training-modules#239 · Opened Jun 25, 2020

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• Link `refinebio-examples/batch-effects` to RNA-seq module

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  Difficulty 2/5 1-3 hours Newbie friendliness 45/100

  AlexsLemonade/training-modules#129 · Opened Jul 16, 2019

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• Include more analogies

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  Difficulty 4/5 3-5 days Newbie friendliness 25/100

  AlexsLemonade/training-modules#122 · 1 comment · Opened Jul 11, 2019

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• two-gene scatterplot

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  Difficulty 3/5 1-2 days Newbie friendliness 35/100

  AlexsLemonade/training-modules#107 · 5 comments · Opened Jul 19, 2018

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