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biocswirl-dev-team / BiocSwirl

BiocSwirl is a series of in-depth swirlify generated courses used to teach bioinformatics workflows in R/Bioconductor using an interactive and easy to digest format. This project was the People's Choice Award for the Vancouver Bioinformatics Hackathon Hackseq2019.
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[biocswirl][dev] Complete course templates #7

Closed lisancao closed 3 years ago

lisancao commented 4 years ago

[biocswirl][dev] Complete course templates

Tasks

Resources

https://swirlstats.com/blog/swirlify.html

e.g.

  1. Concepts in Bioinformatics a. Assay Basic Science (?) i. Considerations for analyses
    1. Organism/Cell Type
    2. Size
    3. Quality b. File types in bioinformatics i. Characteristics of gene file types
    4. File size
    5. Annotation
    6. Metadata ii.
  2. Git, Lab Notebooks
  3. Workflow design
  4. Low level analyses a. Importing, raw data preprocessing, b. Alignment c. Quality Control d. Normalization (with and without spike ins) e. Dimensionality Reduction f. Correcting for batch effects
  5. High Level analyses a. Clustering methods, exploratory analyses
    b. Cell cycle phase classification from gene expression data c. HVG and marker gene identification
  6. Visualizations for high throughput data a. Plots i. tSNE plot b. Heatmaps c. Gene Association Plots (circular plots)
  7. Debugging in Bioinformatics a. Reading error messages
  8. Code Reproducibility a. Open Science Basics
  9. How to determine what packages are up to date and what’s not a. Contributing to open source
  10. Submitting issues and getting support for specific packages

EACH LESSON: BACKGROUND READING + QUESTIONS [THEORY] HANDS-ON CODING AND DEBUGGING [PRACTICE]

Tag can be

biocswirl(related to course material)
biocterm (interface changes)
dev      (developers only)
file     (changes to file and folder structuring) 
rpkg     (r package/usethis and CRAN documentation changes)
feat     (new feature)
fix      (bug fix)
refactor (refactoring code)
style    (formatting, missing semi colons, etc; no code change)
doc      (changes to documentation)
test     (adding or refactoring tests; no production code change)
version  (version bump/new release; no production code change)
dbg      (Changes in debugging code/frameworks; no production code change)
license  (Edits regarding licensing; no production code change)
hack     (Temporary fix to make things move forward; please avoid it)
WIP      (Work In Progress; for intermediate commits to keep patches reasonably sized)