* 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]>