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Update cheatsheet links for intro-R and scRNAseq #521

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merged 23 commits into from
Mar 1, 2022
Merged

Update cheatsheet links for intro-R and scRNAseq #521

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1cd02ca
Links updated for intro-to-R-tidyverse-cheatsheet
sjspielman Feb 25, 2022
d8a5a3d
Removed HTMLs which we do not save. Updated scRNA cheatsheet EXCEPT f…
sjspielman Feb 25, 2022
f62abe7
Removed yaml
sjspielman Feb 28, 2022
53b41de
Add function to ggplot section of cheatsheet, as discussed in Issue …
sjspielman Feb 28, 2022
978b566
Update module-cheatsheets/intro-to-R-tidyverse-cheatsheet.md
sjspielman Feb 28, 2022
d201194
Update module-cheatsheets/intro-to-R-tidyverse-cheatsheet.md
sjspielman Feb 28, 2022
77eb6fb
Update module-cheatsheets/scRNA-seq-cheatsheet.md
sjspielman Feb 28, 2022
f303167
Update module-cheatsheets/scRNA-seq-cheatsheet.md
sjspielman Feb 28, 2022
f19c4ae
Fixed normalize link
sjspielman Feb 28, 2022
cc40f7b
Updates to intro cheatsheet
sjspielman Feb 28, 2022
14a9e53
PDFs of updated cheatsheets with MacDown. Also added blurb to scRNA-s…
sjspielman Mar 1, 2022
9c15f26
we use macdown for pdfs
sjspielman Mar 1, 2022
c444097
Dictionary updates for cheatsheet README
sjspielman Mar 1, 2022
f7ca9c1
Removed cheatsheet readme and fleshed out section in CONTRIBUTING
sjspielman Mar 1, 2022
1beccc7
Update components/dictionary.txt
sjspielman Mar 1, 2022
88d78d7
doctoc'd CONTRIBUTING
sjspielman Mar 1, 2022
3535f53
markdown words back into the dictionary
sjspielman Mar 1, 2022
163bf0f
Update components/dictionary.txt
sjspielman Mar 1, 2022
0431341
Update CONTRIBUTING.md
sjspielman Mar 1, 2022
8ba3de6
rm ggplot from scRNA-seq, include hline and vline geoms in intro chea…
sjspielman Mar 1, 2022
5f1175b
Update CONTRIBUTING.md
sjspielman Mar 1, 2022
31ee52a
go away md
sjspielman Mar 1, 2022
0c883d4
PDF formatting fixed
sjspielman Mar 1, 2022
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16 changes: 16 additions & 0 deletions CONTRIBUTING.md
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Expand Up @@ -17,6 +17,8 @@
- [Files stored on S3](#files-stored-on-s3)
- [Development with `renv`](#development-with-renv)
- [Typical development workflow](#typical-development-workflow)
- [Steps for creating renv.lock only changes pull requests](#steps-for-creating-renvlock-only-changes-pull-requests)
- [Multiple renv.lock changes from multiple branches](#multiple-renvlock-changes-from-multiple-branches)
- [How we use `renv` with Docker](#how-we-use-renv-with-docker)
- [Docker Image](#docker-image)
- [Developing within the Docker container](#developing-within-the-docker-container)
Expand All @@ -26,6 +28,7 @@
- [Spell check](#spell-check)
- [Rendering Test](#rendering-test)
- [Generation of live notebooks and rendering](#generation-of-live-notebooks-and-rendering)
- [Cheatsheets](#cheatsheets)

<!-- END doctoc generated TOC please keep comment here to allow auto update -->

Expand Down Expand Up @@ -237,3 +240,16 @@ This action first downloads input files for the notebooks from S3, so if there a
After a pull request with changes to notebook files has been merged to master, we use the `make-live.yml` workflow to render current versions of the notebooks to html and to make the `-live.Rmd` versions of the files for training sessions.
This workflow then files a PR to `master` with the rendered and live files.
`make-live.yml` is currently manually triggered, but will likely change to running automatically on each PR with changes to notebook files in the near future.


## Cheatsheets

Training modules have corresponding cheatsheets in `module-cheatsheets`.
Cheatsheets are written in plain markdown and can be converted to a shareable PDF format interactively as follows:

+ Be on a MacOS computer
+ Install and/or open the [MacDown program](https://macdown.uranusjr.com/)
+ Open a md cheatsheet in MacDown, and go to `File` -> `Export` -> `PDF`
+ Save appropriately and voila!

When choosing documentation links to incorporate in cheatsheets, we prefer to use [`https://rdrr.io/`](https://rdrr.io/) when possible for Base R and Bioconductor, and we prefer to use [https://www.tidyverse.org/](`https://www.tidyverse.org/`) for `tidyverse` functions.
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2 changes: 2 additions & 0 deletions components/dictionary.txt
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Expand Up @@ -184,6 +184,8 @@ lv
LV
LVs
lysis
MacDown
MacOS
macrophage
Malhotra
McInnes
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