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Publish all current staging branch changes (#442)
* 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 d9f688f68448ef69fe4c1caa48af23051cd7f4e3.
* Revert "Try another test"
This reverts commit 845cf1aff92ea7b83f402bbefd563562b44e5eac.
* 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 d9f688f68448ef69fe4c1caa48af23051cd7f4e3.
* 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 6a38574d312cee82c90c3c036ac9033f9af7f7ec.
* 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 <dv.prasad991@gmail.com>
* 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 8b81fdd96eeecf1d0e479d7908376b8e57dc356d.
* 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 <cansav09@gmail.com>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
* Adding basic footer (#307)
* 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 <dv.prasad991@gmail.com>
* Make the footer retrieve step consistent with others
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
* Updating CONTRIBUTING.md with instructions about staging -> master set 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 <dv.prasad991@gmail.com>
* 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 <dv.prasad991@gmail.com>
* New PR templates to help with new process (#334)
* 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
* Try a "main PR" strategy with links to the real PR templates (#337)
* 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 <43576623+cbethell@users.noreply.github.com>
Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com>
* Add contributing diagrams (#333)
* 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 <dv.prasad991@gmail.com>
* 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 :warning: into :x: in diagrams
* Update all img commit ids
* Address comments from @cbethell 's review
* One little wording update
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
* Make the "Other" PR template the default (#341)
* Make the "Other" PR template the default
* Use jashapiro's wording suggestions
* Add timeline reminder to issue template (#342)
* Pr 1 of 2: Add Microarray Pathway Analysis - GSEA example (#345)
* 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 <dv.prasad991@gmail.com>
* 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 d9f688f68448ef69fe4c1caa48af23051cd7f4e3.
* Revert "Try another test"
This reverts commit 845cf1aff92ea7b83f402bbefd563562b44e5eac.
* 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 d9f688f68448ef69fe4c1caa48af23051cd7f4e3.
* 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 6a38574d312cee82c90c3c036ac9033f9af7f7ec.
* 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 <dv.prasad991@gmail.com>
* 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 8b81fdd96eeecf1d0e479d7908376b8e57dc356d.
* 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 <cansav09@gmail.com>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com>
* 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 <jaclyn.n.taroni@gmail.com>
* rerun snakefile to update rendered html
Co-authored-by: Candace Savonen <cansav09@gmail.com>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
* Pr 2 of 2: Add Microarray Pathway Analysis - GSEA example (#347)
* 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 <dv.prasad991@gmail.com>
* 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 d9f688f68448ef69fe4c1caa48af23051cd7f4e3.
* Revert "Try another test"
This reverts commit 845cf1aff92ea7b83f402bbefd563562b44e5eac.
* 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 d9f688f68448ef69fe4c1caa48af23051cd7f4e3.
* 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 6a38574d312cee82c90c3c036ac9033f9af7f7ec.
* 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 <dv.prasad991@gmail.com>
* 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 8b81fdd96eeecf1d0e479d7908376b8e57dc356d.
* 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 <cansav09@gmail.com>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com>
* 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 <cansav09@gmail.com>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
* Delete intro Rmd and renumber (#355)
* Try out intro and fix filenames
* Undo intro paragraph for now. Too much
* Missed one link to update in GSEA
* Add words about Draft and Refined PRs to CONTRIBUTING.md (#361)
* 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?
* WGCNA Part 1: Set up (#358)
* 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 7560c2a7cb861aaecefd8d241db209d8b3658989.
* 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
* WGCNA Part 2: Running WGCNA (#360)
* 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 <actions@github.com>
* Add pathway analysis intro paragraph to microarray ORA (#356)
* 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
* Fix WGCNA installation (#366)
* Move order of install for WGCNA
* warn moar
* Pr 1 of 2: Add Microarray Pathway Analysis - GSVA example (#359)
* 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 <dv.prasad991@gmail.com>
* 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 d9f688f68448ef69fe4c1caa48af23051cd7f4e3.
* Revert "Try another test"
This reverts commit 845cf1aff92ea7b83f402bbefd563562b44e5eac.
* 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 d9f688f68448ef69fe4c1caa48af23051cd7f4e3.
* 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 6a38574d312cee82c90c3c036ac9033f9af7f7ec.
* 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 <dv.prasad991@gmail.com>
* 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 8b81fdd96eeecf1d0e479d7908376b8e57dc356d.
* 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 <cansav09@gmail.com>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com>
* 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 <jaclyn.n.taroni@gmail.com>
* incorporate the rest of jaclyn-taroni's review suggestions
Co-authored-by: Candace Savonen <cansav09@gmail.com>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
Co-authored-by: GitHub Actions <actions@github.com>
Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
* WGCNA Part 3: DE and heatmaps (#363)
* 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 8b9d57ce13ff2b6b6c5ddbb0169a794f6bbd36de.
* 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 <actions@github.com>
* WGCNA Part 4: Warn about Outliers (#364)
* 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 <actions@github.com>
* Microarray ORA Restructure Instruction (#377)
* 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
* WGCNA Part 5: switch dataset (#379)
* 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 <actions@github.com>
* Change pdf -> png and rereun (#382)
* Pr 2 of 2: Add Microarray Pathway Analysis - GSVA example (#362)
* 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 <dv.prasad991@gmail.com>
* 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 d9f688f68448ef69fe4c1caa48af23051cd7f4e3.
* Revert "Try another test"
This reverts commit 845cf1aff92ea7b83f402bbefd563562b44e5eac.
* 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 d9f688f68448ef69fe4c1caa48af23051cd7f4e3.
* 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 6a38574d312cee82c90c3c036ac9033f9af7f7ec.
* 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 <dv.prasad991@gmail.com>
* 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 8b81fdd96eeecf1d0e479d7908376b8e57dc356d.
* 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 <cansav09@gmail.com>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com>
* 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 <jaclyn.n.taroni@gmail.com>
* add reminder of `gsva_results` format
- cite gsva package vignette
- add more detail around "appropriate format" for plotting
Co-authored-by: Candace Savonen <cansav09@gmail.com>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
Co-authored-by: GitHub Actions <actions@github.com>
Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
* Remove getting started zip file (#392)
* ORA RNA-seq: Part 1 - The Set Up (#394)
* 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
* ORA RNA-seq: Part 2 - Run ORA and get results! (#395)
* 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 mute chatty blocks (#398)
* Add message=FALSE to library loading chunks
* Rerender html files
* Spell check fixes
* rerender
* add GSVA package to Dockerfile (#401)
* Add rendering options via include.R (#402)
* 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
* GSVA for RNA-seq Part 1: Set up (#403)
* 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
* Link citations in render (#407)
* Add links to citations
* Fix umlaut
* Try different strategy for ortholog file download (#411)
* Try different download strategy
* Couple edits
* Move link to before download
* One other wording change
* Editing/polish of microarray heatmap notebook (#409)
* 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 (#414)
* Carry over common comment changes
* Style Rmds
* White space change to force check
Co-authored-by: GitHub Actions <actions@github.com>
* Use same download.file strategy for ortholog RNA-seq example (#413)
* Copy over changes from #411 but make it mouse
* "automatically" gets deleted
* GSVA for RNA-seq: Part 2 -- GSVA and a heatmap (#404)
* 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
* RNA-seq DGE dataset switch (#416)
* Introduce SRP123625
* Updating wording and some other items
* Re-render it
* Spell error fixes
* jashapiro review suggestions
* one more change and re-render
* add part 1 of RNA-seq GSEA example notebook (take 2) (#419)
* PCA polishing edits (#421)
* 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 <cansav09@gmail.com>
* Don't call it a matrix
it's been here for years
* rerender
Co-authored-by: Candace Savonen <cansav09@gmail.com>
* Try out a different download strategy for ORA (#418)
* Change download steps to download file
* re-render
* Spell error fixes
* Use jashapiro wording
* Use download.file for the three other notebooks (#422)
* Bring over the GSEA changes
* Add download.file() to the other three places
* Found a typo
* Fix two things cbethell mentioned in review
* PR 2 of 2: Add RNA-seq Pathway Analysis - GSEA example (take 2) (#420)
* add part 2 of RNA-seq GSEA example notebook (take 2)
* rerun snakefile
* incorporate jaclyn-taroni's review suggestions
* rerun Snakefile to fix html output (#424)
* Umap polish (#423)
* UMAP polish edits
* rendering
* Apply suggestions from code review
Co-authored-by: Candace Savonen <cansav09@gmail.com>
* rerender
* Move filtering to before DESeq2 object creation (#425)
* re-render it
* Further fix merge conflicts and re-render
* Address jashapiro comments
* Heatmap polish (#426)
* Polishing edits to heatmap pages
* Style and render
* OSPL fix
Co-authored-by: Candace Savonen <cansav09@gmail.com>
* rownames -> row names
* rerender all the things
and delete a stray space
* Polish differential exp microarray notebooks (#427)
* 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 Polish Diff Expr RNAseq (#429)
* Minor polishing to RNAseq Diff Expr
* render changes
* Apply suggestions from code review
Co-authored-by: Candace Savonen <cansav09@gmail.com>
* render
Co-authored-by: Candace Savonen <cansav09@gmail.com>
* Polish the microarray ORA notebook (#430)
* Update MSigDB section + rerender
Also fixes long comments and rownames.print=FALSE
* A few more edits to comments
* Part 1: Add rownames.print = FALSE where its helpful (#431)
* Add print.rownames = FALSE where its helpful
* Apparently it doesn't affect design matrices
* Push the htmls so that people can actually see them!!!
* Polish the RNA-seq ORA example (#432)
* Add the rownames.print = FALSE and re-render (#433)
Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
* Polish Microarray GSEA example (#434)
* Polish wording and add introductory paragraphs
* A bit more polishing
* Apply suggestions from code review
Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
* Response to code review
* Apply suggestions from code review
Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
* Propagate citation suggestion to multiple pathway notebooks
* Missed these quotes
* A few mapIds() items
Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
* Polish RNA-seq GSEA example (#437)
* Polish wording and add introductory paragraphs
* A bit more polishing
* Apply suggestions from code review
Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
* Response to code review
* Apply suggestions from code review
Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
* 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 <josh.shapiro@ccdatalab.org>
* Let the algorithm handle it
Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
* GHA: Slack us if Docker build or rendering fails (#438)
* 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 4e83ed1e104f0760db40752f9bc9e641f916d374.
* Revert "Add branch for testing"
This reverts commit 06073504426dc1903cf46bb99cc65a3a91894a3c.
* Polish Ensembl Gene ID conversions (bonus reference updates!) (#435)
* 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 <josh.shapiro@ccdatalab.org>
* Response to code review
* Some numeric updates
* Add rendered files
* render update
* Citation update
* Render updates
* add comment & rerender
Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
* Polish microarray GSVA example (#440)
* 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 <cansav09@gmail.com>
* 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 <cansav09@gmail.com>
* Polishing Ortholog notebooks (#436)
* 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 <josh.shapiro@ccdatalab.org>
* 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: https://github.com/AlexsLemonade/refinebio-examples/issues/439#issuecomment-748721625
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 <cansav09@gmail.com>
* Clarify real genes
* add some spelling words
* Revert "Add branch to docker-build-push.yml for render test"
This reverts commit 8e7b6ec868bab71c4ca0ec2f9b21e2be25df978b.
* rendering
* Caught an igor
Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Co-authored-by: Candace Savonen <cansav09@gmail.com>
* Polish the RNA-seq GSVA example (#441)
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
Co-authored-by: dvenprasad <dv.prasad991@gmail.com>
Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Co-authored-by: GitHub Actions <actions@github.com>- Loading branch information
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