* Update github actions to reflect staging branch

* Add libglpk40 to Dockerfile

* Make it gh-pages-stages!

* Remove dockerfile change that should have been on its own all along

* Does this work?

* Declare a uses

* Switch how env is declared

* Force it to run so we can test it

* try no curly brackets

* What's up with the branch

* Move to bash if instead

* Need quotes?

* forgot a `then`

* Try dollar signs

* Doesn't like the `.`?

* Use curly brackets

* Try ${GITHUB_REF}

* Try ${BRANCH_NAME}

* try ${GITHUB_REF#refs/*/}

* use jashapiro suggestion

* Change to base ref

* Change back to `github.ref`

* Get rid of PR `on:`

* Try another test

* Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316)

* Add lib package 40 thing that clusterprofiler needs

* Try adding options(warn = 2)

* Test if options(warn =2) means it breaks like it should

* Revert "Test if options(warn =2) means it breaks like it should"

This reverts commit d9f688f.

* Revert "Try another test"

This reverts commit 845cf1a.

* Try adding google analytics

* Add to header using includes

* temporary file snuck in there

* Restore master version so they aren't in the review

* Let's call an html file and html file

* Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316)

* Add lib package 40 thing that clusterprofiler needs

* Try adding options(warn = 2)

* Test if options(warn =2) means it breaks like it should

* Revert "Test if options(warn =2) means it breaks like it should"

This reverts commit d9f688f.

For simplicity, we will now run this even if the dockerfile hasn't changed.

This reverts commit 6a38574.

Okay, so the branch name is now inaccurate, but that is fine...

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

…fashion

…g-docker

Stop staging from pushing to dockerhub

Bring refine.bio fashion to staging too: attempt 2

* Add some rough draft issue templates

* Incorporate cbethell review

* Get rid of `Other` labels that aren't useful

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Update microarray and RNAseq overview figures


- add context re figures
- change .jpg to .png for consistency

* Revert "Mechanics for CSS file and navbar add feedback URL (#303)"

This reverts commit 8b81fdd.

* update links to diagrams

* @dvenprasad updated figure spacing

* add the right updated figure

* replace section of link to figures with updated commit id

* incorporate @cansavvy's suggested changes

Co-authored-by: Candace Savonen <[email protected]>
Co-authored-by: dvenprasad <[email protected]>

* It works!

* Add feedback url

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Make the footer retrieve step consistent with others

Co-authored-by: dvenprasad <[email protected]>

…t up (#313)

* Updating contributing with info about staging branch

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Add more details to CONTRIBUTING about cherry picks and etc

* Add bit about html preview

* Incorporate Josh comment and drop log.log

* Add bit about a hotfixes to staging PRs

* Incorporate jashapiro feedback

* Incorporate a few more bits of jashapiro feedback

* Update doctoc

* Make pull requests section H2

* Incorporate jashapiro suggestion to be make more specific branch names

* Meh, we don't need <>

* Change to use "publish" instead of "live"

* Re DocToc

* Add a bit more direction about PR base branches

* Adjust links

* Missed one link

Co-authored-by: dvenprasad <[email protected]>

* Add basic templates

* make it live PR template

* Add html preview

* Add one more "other" template

* Minor edit

* Polish up some things. Add "PR stage"

* Minor edits

* Implement cbethell review

* Get rid of headers and try a "main PR" thing.

* Rearrange order

* Links don't work per se

* Try href strategy?

* Update .github/PULL_REQUEST_TEMPLATE.md

Co-authored-by: Chante Bethell  <[email protected]>

Co-authored-by: Chante Bethell  <[email protected]>

* Updating contributing with info about staging branch

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Add more details to CONTRIBUTING about cherry picks and etc

* Add bit about html preview

* Incorporate Josh comment and drop log.log

* Add bit about a hotfixes to staging PRs

* Incorporate jashapiro feedback

* Incorporate a few more bits of jashapiro feedback

* Add the PR diagrams

* Add diagrams and some words about them to CONTRIBUTING.md

* Couple minor edits

* Update doctoc

* Make pull requests section H2

* Incorporate jashapiro suggestion to be make more specific branch names

* Meh, we don't need <>

* Change to use "publish" instead of "live"

* Update diagrams to say "publish"

* re doctoc

* Some polishing of wording

* Make robot emoji a png so it renders

* Update commit ids

* A little more words

* Make headlnes more parallel

* Couple little updates

* A couple more polishing items

* Turn ⚠️ into ❌ in diagrams

* Update all img commit ids

* Address comments from @cbethell 's review

* One little wording update

Co-authored-by: dvenprasad <[email protected]>

* Make the "Other" PR template the default

* Use jashapiro's wording suggestions

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Making staging changes live (#329)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Update github actions to reflect staging branch (#311)

* Update github actions to reflect staging branch

* Add libglpk40 to Dockerfile

* Make it gh-pages-stages!

* Remove dockerfile change that should have been on its own all along

* Does this work?

* Declare a uses

* Switch how env is declared

* Force it to run so we can test it

* try no curly brackets

* What's up with the branch

* Move to bash if instead

* Need quotes?

* forgot a `then`

* Try dollar signs

* Doesn't like the `.`?

* Use curly brackets

* Try ${GITHUB_REF}

* Try ${BRANCH_NAME}

* try ${GITHUB_REF#refs/*/}

* use jashapiro suggestion

* Change to base ref

* Change back to `github.ref`

* Get rid of PR `on:`

* Try another test

* Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316)

* Add lib package 40 thing that clusterprofiler needs

* Try adding options(warn = 2)

* Test if options(warn =2) means it breaks like it should

* Revert "Test if options(warn =2) means it breaks like it should"

This reverts commit d9f688f.

* Revert "Try another test"

This reverts commit 845cf1a.

* Add google analytics to renderings (#314)

* Try adding google analytics

* Add to header using includes

* temporary file snuck in there

* Restore master version so they aren't in the review

* Let's call an html file and html file

* Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316)

* Add lib package 40 thing that clusterprofiler needs

* Try adding options(warn = 2)

* Test if options(warn =2) means it breaks like it should

* Revert "Test if options(warn =2) means it breaks like it should"

This reverts commit d9f688f.

* Only push if we are in master.

For simplicity, we will now run this even if the dockerfile hasn't changed.

* Add test target

* test staging workflow with this branch

* back to latest tag

* Try separate push step

* change tags to test push

* Revert "change tags to test push"

This reverts commit 6a38574.

* Remove this branch from triggers

* Push staging, retag and push master

Okay, so the branch name is now inaccurate, but that is fine...

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

* Update scripts/render-notebooks.R

* Add some issue templates (#319)

* Add some rough draft issue templates

* Incorporate cbethell review

* Get rid of `Other` labels that aren't useful

* Update diagrams showing how microarray/RNA-seq work  (#326)

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Update microarray and RNAseq overview figures


- add context re figures
- change .jpg to .png for consistency

* Revert "Mechanics for CSS file and navbar add feedback URL (#303)"

This reverts commit 8b81fdd.

* update links to diagrams

* @dvenprasad updated figure spacing

* add the right updated figure

* replace section of link to figures with updated commit id

* incorporate @cansavvy's suggested changes

Co-authored-by: Candace Savonen <[email protected]>
Co-authored-by: dvenprasad <[email protected]>

Co-authored-by: Joshua Shapiro <[email protected]>
Co-authored-by: dvenprasad <[email protected]>
Co-authored-by: Chante Bethell <[email protected]>

* add first half of microarray GSEA example nb

- add first part of new GSEA notebook example
- update Snakefile
- update navbar file
- update `references.bib`
- update `dictionary.txt`

* revert commit that snuck in

* revert second commit that snuck in

* fix render notebooks merge conflict

* incorporate cansavvy's review suggestions

* add step handling duplicate ids 

- add note re using said approach

* update comment

* replace lfc with t-statistic value where mentioned

* incorporate @cansavvy's review suggestions

- fix typo 
- add sanity check when removing duplicates

* replace `!duplicated()` with `dplyr::distinct()`

* incorporate @jaclyn-taroni's review suggestions

- add preview of `dr_hallmark_df`
- add context where needed 
- adapt approach to removing duplicate gene ids

* add a bit more context re removing dup gene IDs

* use absolute value of t-statistic

* Apply GSEA explanation suggestion from code review

Co-authored-by: Jaclyn Taroni <[email protected]>

* rerun snakefile to update rendered html

Co-authored-by: Candace Savonen <[email protected]>
Co-authored-by: dvenprasad <[email protected]>
Co-authored-by: Joshua Shapiro <[email protected]>
Co-authored-by: Jaclyn Taroni <[email protected]>

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Making staging changes live (#329)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Update github actions to reflect staging branch (#311)

* Update github actions to reflect staging branch

* Add libglpk40 to Dockerfile

* Make it gh-pages-stages!

* Remove dockerfile change that should have been on its own all along

* Does this work?

* Declare a uses

* Switch how env is declared

* Force it to run so we can test it

* try no curly brackets

* What's up with the branch

* Move to bash if instead

* Need quotes?

* forgot a `then`

* Try dollar signs

* Doesn't like the `.`?

* Use curly brackets

* Try ${GITHUB_REF}

* Try ${BRANCH_NAME}

* try ${GITHUB_REF#refs/*/}

* use jashapiro suggestion

* Change to base ref

* Change back to `github.ref`

* Get rid of PR `on:`

* Try another test

* Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316)

* Add lib package 40 thing that clusterprofiler needs

* Try adding options(warn = 2)

* Test if options(warn =2) means it breaks like it should

* Revert "Test if options(warn =2) means it breaks like it should"

This reverts commit d9f688f.

* Revert "Try another test"

This reverts commit 845cf1a.

* Add google analytics to renderings (#314)

* Try adding google analytics

* Add to header using includes

* temporary file snuck in there

* Restore master version so they aren't in the review

* Let's call an html file and html file

* Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316)

* Add lib package 40 thing that clusterprofiler needs

* Try adding options(warn = 2)

* Test if options(warn =2) means it breaks like it should

* Revert "Test if options(warn =2) means it breaks like it should"

This reverts commit d9f688f.

* Only push if we are in master.

For simplicity, we will now run this even if the dockerfile hasn't changed.

* Add test target

* test staging workflow with this branch

* back to latest tag

* Try separate push step

* change tags to test push

* Revert "change tags to test push"

This reverts commit 6a38574.

* Remove this branch from triggers

* Push staging, retag and push master

Okay, so the branch name is now inaccurate, but that is fine...

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

* Update scripts/render-notebooks.R

* Add some issue templates (#319)

* Add some rough draft issue templates

* Incorporate cbethell review

* Get rid of `Other` labels that aren't useful

* Update diagrams showing how microarray/RNA-seq work  (#326)

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Update microarray and RNAseq overview figures


- add context re figures
- change .jpg to .png for consistency

* Revert "Mechanics for CSS file and navbar add feedback URL (#303)"

This reverts commit 8b81fdd.

* update links to diagrams

* @dvenprasad updated figure spacing

* add the right updated figure

* replace section of link to figures with updated commit id

* incorporate @cansavvy's suggested changes

Co-authored-by: Candace Savonen <[email protected]>
Co-authored-by: dvenprasad <[email protected]>

Co-authored-by: Joshua Shapiro <[email protected]>
Co-authored-by: dvenprasad <[email protected]>
Co-authored-by: Chante Bethell <[email protected]>

* add latter half of GSEA microarray example (includes GSEA steps)

fix merge conflicts

* add incode prompt

* revert commit that snuck in

* revert commit

* set seed and re-run

* incorporate some of the wording/context suggestions from review

* rerun Snakefile

* incorporate suggested changes re additional context/GSEA explanation

* implement `top_n()`

* add a bit more context for clarification re ES score

* update GSEA explanation before gene ID conversion section

* incorporate @cansavvy's wording suggestions

* mimic "highly" -> "most" language

* incorporate wording suggestions from code review

* some re-structuring/re-wording based on review suggestions

* update `dictionary.txt` file

* incorporate @jaclyn-taroni's review suggestions

Co-authored-by: Candace Savonen <[email protected]>
Co-authored-by: dvenprasad <[email protected]>
Co-authored-by: Joshua Shapiro <[email protected]>

* Try out intro and fix filenames

* Undo intro paragraph for now. Too much

* Missed one link to update in GSEA

* Explicitly discuss draft vs refine PRs in contrib

* doctoc it

* Remove asterisks

* Refine wording

* Use cbethell's wording suggestions

* Make that one sentence more clear?

* Put in basic changes: navbar, dict, snakefile, Rmd

* More polishing and info and refs

* Update file paths

* Bring back docker changes

* Add to dictionary

* Add a couple refs

* Add ref and other little things

* Revert "Add ref and other little things"

This reverts commit 7560c2a.

* Address straightforward comments from cbethell

* Add ref

* Add more refs and re-render

* Remove that extra part that should only be in part2 not here

* Incorporate jashapiro review

* Shorten up some more comments

* rowSums!!

* Get rid of tibble step and change wording

* Put in basic changes: navbar, dict, snakefile, Rmd

* More polishing and info and refs

* Update file paths

* Bring back docker changes

* Add to dictionary

* Add a couple refs

* Add next steps

* Add some polishing and refs

* Address the straightforward items from cbethell 's review

* Incorporate jashapiro review from #358

* Style Rmds

* Bring over part1 changes and re-render

* Edit things based on jashapiro review

Co-authored-by: GitHub Actions <[email protected]>

* Try out intro and fix filenames

* Undo intro paragraph for now. Too much

* Add intro paragraph

* Fix typo, add links

* Incorporate cbethell review

* Wording change from @envest

* Move order of install for WGCNA

* warn moar

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Making staging changes live (#329)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Update github actions to reflect staging branch (#311)

* Update github actions to reflect staging branch

* Add libglpk40 to Dockerfile

* Make it gh-pages-stages!

* Remove dockerfile change that should have been on its own all along

* Does this work?

* Declare a uses

* Switch how env is declared

* Force it to run so we can test it

* try no curly brackets

* What's up with the branch

* Move to bash if instead

* Need quotes?

* forgot a `then`

* Try dollar signs

* Doesn't like the `.`?

* Use curly brackets

* Try ${GITHUB_REF}

* Try ${BRANCH_NAME}

* try ${GITHUB_REF#refs/*/}

* use jashapiro suggestion

* Change to base ref

* Change back to `github.ref`

* Get rid of PR `on:`

* Try another test

* Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316)

* Add lib package 40 thing that clusterprofiler needs

* Try adding options(warn = 2)

* Test if options(warn =2) means it breaks like it should

* Revert "Test if options(warn =2) means it breaks like it should"

This reverts commit d9f688f.

* Revert "Try another test"

This reverts commit 845cf1a.

* Add google analytics to renderings (#314)

* Try adding google analytics

* Add to header using includes

* temporary file snuck in there

* Restore master version so they aren't in the review

* Let's call an html file and html file

* Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316)

* Add lib package 40 thing that clusterprofiler needs

* Try adding options(warn = 2)

* Test if options(warn =2) means it breaks like it should

* Revert "Test if options(warn =2) means it breaks like it should"

This reverts commit d9f688f.

* Only push if we are in master.

For simplicity, we will now run this even if the dockerfile hasn't changed.

* Add test target

* test staging workflow with this branch

* back to latest tag

* Try separate push step

* change tags to test push

* Revert "change tags to test push"

This reverts commit 6a38574.

* Remove this branch from triggers

* Push staging, retag and push master

Okay, so the branch name is now inaccurate, but that is fine...

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

* Update scripts/render-notebooks.R

* Add some issue templates (#319)

* Add some rough draft issue templates

* Incorporate cbethell review

* Get rid of `Other` labels that aren't useful

* Update diagrams showing how microarray/RNA-seq work  (#326)

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Update microarray and RNAseq overview figures


- add context re figures
- change .jpg to .png for consistency

* Revert "Mechanics for CSS file and navbar add feedback URL (#303)"

This reverts commit 8b81fdd.

* update links to diagrams

* @dvenprasad updated figure spacing

* add the right updated figure

* replace section of link to figures with updated commit id

* incorporate @cansavvy's suggested changes

Co-authored-by: Candace Savonen <[email protected]>
Co-authored-by: dvenprasad <[email protected]>

Co-authored-by: Joshua Shapiro <[email protected]>
Co-authored-by: dvenprasad <[email protected]>
Co-authored-by: Chante Bethell <[email protected]>

* Add first half of microarray GSVA example notebook

* add packages to Dockerfile and rerun

* fix reference

* add to navbar

* remove mention of pheatmap

* incorporate @jaclyn-taroni's suggestion on collapsing duplicates logic

* incorporate cansavvy's review comments

- fix logic combing rest of mapped data with the collapsed duplicates data
- fix context around that logic

* clarify/change some wording based on cansavvy's suggestions

* incorporate single sample example of selecting max expression values

* Push code that cbethell and I chatted through

* Add to dictionary

* Style Rmds

* rerun Snakefile to update html file

* Apply jaclyn-taroni's wording suggestions from code review

Co-authored-by: Jaclyn Taroni <[email protected]>

* incorporate the rest of jaclyn-taroni's review suggestions

Co-authored-by: Candace Savonen <[email protected]>
Co-authored-by: dvenprasad <[email protected]>
Co-authored-by: Joshua Shapiro <[email protected]>
Co-authored-by: GitHub Actions <[email protected]>
Co-authored-by: Jaclyn Taroni <[email protected]>

* Put in basic changes: navbar, dict, snakefile, Rmd

* More polishing and info and refs

* Update file paths

* Bring back docker changes

* Add to dictionary

* Add a couple refs

* Add next steps

* Add some polishing and refs

* Address the straightforward items from cbethell 's review

* Incorporate jashapiro review from #358

* Style Rmds

* Bring over part1 changes and re-render

* Add last set of steps

* Push this partcular plot version in case we wanna come back to it

* Commit this multiple module pheatmap in case I want to return to it

* ComplexHeatmap is mostly wrangled

* It's working!

* Save to PDFs

* Fix color function and re-render

* Add outlier thing

* Revert "Add outlier thing"

This reverts commit 8b9d57c.

* Add ref for ComplexHeatmap

* Incorporate jashapiro review and rerender

* Remove standardize_genes option

* Wrap up those last few typo things

Co-authored-by: GitHub Actions <[email protected]>

* Put in basic changes: navbar, dict, snakefile, Rmd

* More polishing and info and refs

* Update file paths

* Bring back docker changes

* Add to dictionary

* Add a couple refs

* Add next steps

* Add some polishing and refs

* Address the straightforward items from cbethell 's review

* Incorporate jashapiro review from #358

* Style Rmds

* Bring over part1 changes and re-render

* Add last set of steps

* Push this partcular plot version in case we wanna come back to it

* Commit this multiple module pheatmap in case I want to return to it

* ComplexHeatmap is mostly wrangled

* It's working!

* Save to PDFs

* Fix color function and re-render

* Add outlier thing

* Style Rmds

* Re-rendered html

* switch the whole outlier thing to just a comment

* re-render after staging merge

Co-authored-by: GitHub Actions <[email protected]>

* Some edits and adding other tutorials

* Add more guidance about why pick ORA

* A bit more word changing

* A few more wording edits

* Incorporating jashapiro review

* Get rid of other GSEA mention

* sessioninfo::session_info()

* Put those two wording things in jashapiro mentioned

* switch wording and dataset in general

* Few more wording edits

* Update dictionary; fix spelling errors

* Re-render!

* Change to 7 and incorporate jashapiro review

* Also switch the most sig module!

* Two comments from jashapiro review

* Put the comments too

* Style Rmds

* Use all_of() to get rid warning

* Style Rmds

* Re-render

Co-authored-by: GitHub Actions <[email protected]>

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Making staging changes live (#329)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Update github actions to reflect staging branch (#311)

* Update github actions to reflect staging branch

* Add libglpk40 to Dockerfile

* Make it gh-pages-stages!

* Remove dockerfile change that should have been on its own all along

* Does this work?

* Declare a uses

* Switch how env is declared

* Force it to run so we can test it

* try no curly brackets

* What's up with the branch

* Move to bash if instead

* Need quotes?

* forgot a `then`

* Try dollar signs

* Doesn't like the `.`?

* Use curly brackets

* Try ${GITHUB_REF}

* Try ${BRANCH_NAME}

* try ${GITHUB_REF#refs/*/}

* use jashapiro suggestion

* Change to base ref

* Change back to `github.ref`

* Get rid of PR `on:`

* Try another test

* Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316)

* Add lib package 40 thing that clusterprofiler needs

* Try adding options(warn = 2)

* Test if options(warn =2) means it breaks like it should

* Revert "Test if options(warn =2) means it breaks like it should"

This reverts commit d9f688f.

* Revert "Try another test"

This reverts commit 845cf1a.

* Add google analytics to renderings (#314)

* Try adding google analytics

* Add to header using includes

* temporary file snuck in there

* Restore master version so they aren't in the review

* Let's call an html file and html file

* Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316)

* Add lib package 40 thing that clusterprofiler needs

* Try adding options(warn = 2)

* Test if options(warn =2) means it breaks like it should

* Revert "Test if options(warn =2) means it breaks like it should"

This reverts commit d9f688f.

* Only push if we are in master.

For simplicity, we will now run this even if the dockerfile hasn't changed.

* Add test target

* test staging workflow with this branch

* back to latest tag

* Try separate push step

* change tags to test push

* Revert "change tags to test push"

This reverts commit 6a38574.

* Remove this branch from triggers

* Push staging, retag and push master

Okay, so the branch name is now inaccurate, but that is fine...

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

* Update scripts/render-notebooks.R

* Add some issue templates (#319)

* Add some rough draft issue templates

* Incorporate cbethell review

* Get rid of `Other` labels that aren't useful

* Update diagrams showing how microarray/RNA-seq work  (#326)

* Mechanics for CSS file and navbar add feedback URL (#303)

* Adding in some style with css

* Use css magic

* Try making the navbar blue

* Add survey link

* Make font smaller

* Need a comma

* Change to normalizePath

* normalizepath separate step references.bib

* Move references.bib to component folder

* Made ccs modifications, added logo file

Made changes to css/navbar.html
Tried to add the logo but it but it cuts out and not sure how to make it decent.

* Resolve render-notebooks.R conflict

* Remove testing html from file diff

* uncommented mobile nav

Co-authored-by: dvenprasad <[email protected]>

* Update microarray and RNAseq overview figures


- add context re figures
- change .jpg to .png for consistency

* Revert "Mechanics for CSS file and navbar add feedback URL (#303)"

This reverts commit 8b81fdd.

* update links to diagrams

* @dvenprasad updated figure spacing

* add the right updated figure

* replace section of link to figures with updated commit id

* incorporate @cansavvy's suggested changes

Co-authored-by: Candace Savonen <[email protected]>
Co-authored-by: dvenprasad <[email protected]>

Co-authored-by: Joshua Shapiro <[email protected]>
Co-authored-by: dvenprasad <[email protected]>
Co-authored-by: Chante Bethell <[email protected]>

* Add part two of GSVA microarray example notebook

* update comment

* update violin plot and its interpretation

* add to `dictionary.txt`

* apply significance and multiple hypothesis testing before plotting

* Switching to northcott and a sina plot of one pathway

* Style Rmds

* Re-render it all

* Adjust wording add tidbits about limma and re-render

* Few more wording edits

* Caught a few more little wording issues. Re-rendered

* Remove Murat2008 ref

* Restore the part 1 changes that got lost in the merge

* incorporate most of jaclyn-taroni's suggested changes

- create annotated results df using wide -> long method
- update some wording/context re `mx.diff = TRUE` and what that means

* remove outdated entries in `dictionary.txt`

- remove unnecessary reference in `references.bib`

* fix axis label

* break up `annotated_results_df` steps

* Apply suggestions from code review

Co-authored-by: Jaclyn Taroni <[email protected]>

* add reminder of `gsva_results` format

- cite gsva package vignette
- add more detail around "appropriate format" for plotting

Co-authored-by: Candace Savonen <[email protected]>
Co-authored-by: dvenprasad <[email protected]>
Co-authored-by: Joshua Shapiro <[email protected]>
Co-authored-by: GitHub Actions <[email protected]>
Co-authored-by: Jaclyn Taroni <[email protected]>

* Add the file. It works

* Add components

* re-render

* Add review tags

* Update wording around detectable genes

* Add some words to dictionary.txt

* re-render

* Switch to PNG

* Incorporating cbethell 's and envest 's  review

* Switch from using gene symbols to Entrez IDs

* Isolate to just set up

* Fix Typo

* Polish the wording in a few places

* Incorporate jashapiro reviews and remove tags

* Port one wording change over to microarray ORA

* One more wording edit

* Add the file. It works

* Add components

* re-render

* Add review tags

* Update wording around detectable genes

* Add some words to dictionary.txt

* re-render

* Switch to PNG

* Incorporating cbethell 's and envest 's  review

* Switch from using gene symbols to Entrez IDs

* Couple wording polishes

* Copy over changes from #394 's review

* Use jashapiro wording suggestions, delete tags

* Add message=FALSE to library loading chunks

* Rerender html files

* Spell check fixes

* rerender

* Add option to include R code in an early chunk

* Add the include file when rendering

* Change width to 70

* add example rerender

* comment and naming changes

* Update contributing.md with include file description

* Add all rendered changes

* Scrapbooking together an analysis

* switch back to kcdf = "Gaussian"

* Rearrange based on chat with Jackie

* Fix the two things from jaclyn-taroni partial review

* Few wording edits

* Make the dup checks more relevant

* Make PNG a bit bigger

* incorporate most of jaclyn-taroni review comments

* Try out the msigdbr list thing

* Isolate to first parts of gsva

* Editing explanations

* Fix a couple spelling things

* Incorporate jaclyn-taroni review and delete tags

* Use `vst_df`

* One more wording change

* Remove that instance of "lists" that isn't really what we mean

* Add links to citations

* Fix umlaut

* Try different download strategy

* Couple edits

* Move link to before download

* One other wording change

* Intro edits

* Heatmap edits

* Render changes

* Couple edits that didn't get saved

* One more comment compaction.

* Remove relative links

* Add to microarray strengths

* Carry over common  comment changes

* Style Rmds

* White space change to force check

Co-authored-by: GitHub Actions <[email protected]>

* Copy over changes from #411 but make it mouse

* "automatically" gets deleted

* Scrapbooking together an analysis

* switch back to kcdf = "Gaussian"

* Rearrange based on chat with Jackie

* Fix the two things from jaclyn-taroni partial review

* Few wording edits

* Make the dup checks more relevant

* Make PNG a bit bigger

* incorporate most of jaclyn-taroni review comments

* Try out the msigdbr list thing

* Re-render

* Update based on part 1 review

* Add bit that shows overlaps

* Make wording changes based on jaclyn-taroni review

* Do some wording/explanation edits

* Introduce SRP123625

* Updating wording and some other items

* Re-render it

* Spell error fixes

* jashapiro review suggestions

* one more change and re-render

* Add principal component background

Also shortened code lines and results tables

* Add some more context and explanation of results

* Updates to rnaseq PCA

* Format and rerender

* update screenshots

* Apply suggestions from code review

Co-authored-by: Candace Savonen <[email protected]>

* Don't call it a matrix

it's been here for years

* rerender

Co-authored-by: Candace Savonen <[email protected]>

* Change download steps to download file

* re-render

* Spell error fixes

* Use jashapiro wording

* Bring over the GSEA changes

* Add download.file() to the other three places

* Found a typo

* Fix two things cbethell mentioned in review

* add part 2 of RNA-seq GSEA example notebook (take 2)

* rerun snakefile

* incorporate jaclyn-taroni's review suggestions

* UMAP polish edits

* rendering

* Apply suggestions from code review

Co-authored-by: Candace Savonen <[email protected]>

* rerender

* re-render it

* Further fix merge conflicts and re-render

* Address jashapiro comments

* Polishing edits to heatmap pages

* Style and render

* OSPL fix

Co-authored-by: Candace Savonen <[email protected]>

* rownames -> row names

* rerender all the things

and delete a stray space

* Changes to differential exp microarray notebook

* Spelling updates

* Add comments and releveling, as suggested by @cansavvy

* code formatting updates

embrace the pipe

* remove apeglm

* Add some eBayes info!

* polishing microarray multiple groups

* Rerender everything

* Split off multiple testing

* Rerender

* Minor polishing to RNAseq Diff Expr

* render changes

* Apply suggestions from code review

Co-authored-by: Candace Savonen <[email protected]>

* render

Co-authored-by: Candace Savonen <[email protected]>

* Update MSigDB section + rerender

Also fixes long comments and rownames.print=FALSE

* A few more edits to comments

* Add print.rownames = FALSE where its helpful

* Apparently it doesn't affect design matrices

* Push the htmls so that people can actually see them!!!

Co-authored-by: jashapiro <[email protected]>

* Polish wording and add introductory paragraphs

* A bit more polishing

* Apply suggestions from code review

Co-authored-by: jashapiro <[email protected]>

* Response to code review

* Apply suggestions from code review

Co-authored-by: jashapiro <[email protected]>

* Propagate citation suggestion to multiple pathway notebooks

* Missed these quotes

* A few mapIds() items

Co-authored-by: jashapiro <[email protected]>

* Polish wording and add introductory paragraphs

* A bit more polishing

* Apply suggestions from code review

Co-authored-by: jashapiro <[email protected]>

* Response to code review

* Apply suggestions from code review

Co-authored-by: jashapiro <[email protected]>

* Propagate citation suggestion to multiple pathway notebooks

* Missed these quotes

* A few mapIds() items

* Polish RNA-seq GSEA example

* Missed a long comment

* Update components/references.bib

Co-authored-by: jashapiro <[email protected]>

* Let the algorithm handle it

Co-authored-by: jashapiro <[email protected]>

* Add Slack notification to docker-build-push.yml

* Add Slack notification to docker-build.yml

* Add branch for testing

* Add library load of package not installed

* Revert "Add library load of package not installed"

This reverts commit 4e83ed1.

* Revert "Add branch for testing"

This reverts commit 0607350.

* Polish wording and add introductory paragraphs

* A bit more polishing

* Reference updates

* ensembl gene id polish

* Get out of here capital Refine.bio

* No more bare dfs

* Transfer changes to RNAseq (and some back)

* Apply suggestions from code review

Co-authored-by: jashapiro <[email protected]>

* Response to code review

* Some numeric updates

* Add rendered files

* render update

* Citation update

* Render updates

* add comment & rerender

Co-authored-by: Jaclyn Taroni <[email protected]>

* Ignore the gene_sets directory

* Polish the microarray GSVA example

* Missed a couple mentions of GSEA

* Borrow some polishing from #427

* Apply suggestions from code review

Co-authored-by: Candace Savonen <[email protected]>

* Newline in intro paragraph everywhere

* Add note about model organisms with GSVA

Link to RNA-seq GSVA example

* Rerender notebooks

Co-authored-by: Candace Savonen <[email protected]>

* Polish wording and add introductory paragraphs

* A bit more polishing

* Reference updates

* ensembl gene id polish

* Get out of here capital Refine.bio

* No more bare dfs

* Transfer changes to RNAseq (and some back)

* Apply suggestions from code review

Co-authored-by: jashapiro <[email protected]>

* Response to code review

* Some numeric updates

* Add rendered files

* render update

* Citation update

* Add polishing for ortholog examples

* Transfer intro sentence updates to related notebooks

* more polish - remove duplicates from counts

* Transfer changes to rnaseq

* Rendering updates

* other rendering updates

* Render updates

* Change ftp -> http for ftp.ebi

As noted here: #439 (comment)

Confirmed that this does work as expected by rendering.

* Add branch to docker-build-push.yml for render test

* Apply suggestions from code review

Co-authored-by: Candace Savonen <[email protected]>

* Clarify real genes

* add some spelling words

* Revert "Add branch to docker-build-push.yml for render test"

This reverts commit 8e7b6ec.

* rendering

* Caught an igor

Co-authored-by: Jaclyn Taroni <[email protected]>
Co-authored-by: Candace Savonen <[email protected]>