Polish Microarray GSEA example #434

jaclyn-taroni · 2020-12-16T20:22:19Z

Purpose

Polishing microarray GSEA example.

Issue addressed

For the microarray GSEA example, the following are being addressed:

Enforcing comment character length limit (Enforce code width limit #406)
Updating the section that said it was about clusterProfiler but was really about msigdbr (The "Getting familiar with clusterProfiler's options" section of ORA examples describes msigdbr #415)
Stopping row names from being printed for paged tables (Remove rownames from printed tables #428)
Adding the introductory paragraphs that are in every pathway analysis notebook (Add introductory paragraphs to microarray GSEA example, review text for RNA-seq GSEA example #354)

There is also a good amount of editing happening in this pull request in the spirit of #290.

Directions for the reviewers

I would recommend that the reviewers look at the whole document when reviewing, rather that just the diff, to assess the level of detail and description of methods in the writing.

One concern I have is that the "main" description of how GSEA works is under Purpose of this analysis. Ideally it would be closer to the GSEA() business itself. However, I think we need some explanation of the method before we get down to removing duplicate identifiers. An idea: We could move the description of GSEA that's under Purpose to under the Perform gene set enrichment analysis (GSEA) header and then move the removal of duplicates (and the explanation) to under the Determine our pre-ranked genes list section.

Specific questions

@cbethell - We set the seed in the RNA-seq example, but we didn't here. I added a set.seed() step here, right before we "need" it should someone be viewing this example and have jumped to the analysis code. Is this the correct thing to do?
@jashapiro - you filed Expand "Purpose of this Analysis" #410 and have looked at more examples than me recently! Is this an appropriate level of detail/description in your opinion?

jashapiro

I looked through the first section mostly at this point, and I agree that the GSEA explanation makes more sense a bit later. I might wait for that update to read through more carefully?

I also made some comments on citations that I noticed along the way.

jashapiro · 2020-12-16T20:39:57Z

02-microarray/pathway-analysis_microarray_02_gsea.Rmd

-Genes are ranked from most highly positive to most highly negative, weighted according to their gene-level statistic, which is essential to the calculation of the enrichment score (ES), a pathway-level statistic, for each gene set.
-More specifically, an ES is calculated by starting with the most highly ranked genes (based on the gene-level statistic selected for ranking) and increasing the score when a gene is in the pathway and decreasing the score when a gene is not in the pathway.
-Normalized enrichment scores (NES) are enrichment scores that are scaled to account for gene sets of different sizes [@Subramanian2005; @Korotkevich2019].
+This particular example analysis shows how you can use Gene Set Enrichment Analysis (GSEA) to detect situations where genes in a predefined gene set or pathway change in a coordinated way between two biological states [@Subramanian2005; @GSEA-broad-institute]. 


In looking at the rendered file, it appears that the citation here might need updating. I'm not sure the @GSEA-broad-institute citation is needed, unless we want a link to the website, which I think might be better provided directly? They only ask that you cite Subramanian: http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/FAQ#How_do_I_cite_GSEA.3F

If we do keep that citation, we need to update it so it doesn't render as "Diego and Team" by adding an extra set of brackets. We should also add a year.

author = {{UC San Diego and Broad Institute Team}},

Diego and Team... erasing the contributions of trailblazing young women like Dora, yet again.

jashapiro · 2020-12-16T20:45:21Z

02-microarray/pathway-analysis_microarray_02_gsea.Rmd

+Changes at the pathway-level may be statistically significant, and contribute to phenotypic differences, even if the changes in the expression level of individual genes are small. 
+
+GSEA calculates a pathway-level metric, called an enrichment score (ES), by ranking genes by a gene-level statistic.
+This score reflects whether or not a gene set or pathway is overrepresented at the top or bottom of the gene rankings [@clusterProfiler-book]. 


@clusterProfiler-book needs a year as well... a bit annoying when they don't give you a way they want to be cited!

I just added 2020? I don't know what else we would use.

02-microarray/pathway-analysis_microarray_02_gsea.Rmd

jashapiro · 2020-12-16T20:49:28Z

02-microarray/pathway-analysis_microarray_02_gsea.Rmd

+This particular example analysis shows how you can use Gene Set Enrichment Analysis (GSEA) to detect situations where genes in a predefined gene set or pathway change in a coordinated way between two biological states [@Subramanian2005; @GSEA-broad-institute]. 
+Changes at the pathway-level may be statistically significant, and contribute to phenotypic differences, even if the changes in the expression level of individual genes are small. 
+
+GSEA calculates a pathway-level metric, called an enrichment score (ES), by ranking genes by a gene-level statistic.


Can I suggest we never use "ES" and always just use the full phrase?

Sure, but we absolutely will have to say NES because of what GSEA() returns...

Yeah, in the context of a variable, it is unavoidable...

jashapiro · 2020-12-16T20:52:59Z

02-microarray/pathway-analysis_microarray_02_gsea.Rmd

-Normalized enrichment scores (NES) are enrichment scores that are scaled to account for gene sets of different sizes [@Subramanian2005; @Korotkevich2019].
+This particular example analysis shows how you can use Gene Set Enrichment Analysis (GSEA) to detect situations where genes in a predefined gene set or pathway change in a coordinated way between two biological states [@Subramanian2005; @GSEA-broad-institute]. 
+Changes at the pathway-level may be statistically significant, and contribute to phenotypic differences, even if the changes in the expression level of individual genes are small. 
+


I'm thinking that this may be a reasonable place to stop for the "Purpose" section. The content below is getting into details of the method, that I think that would make sense to move to the "Perform GSEA section", as you suggest in your initial comments.

Okay! I'll give rearranging a try.

Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>

jaclyn-taroni · 2020-12-17T13:25:36Z

02-microarray/pathway-analysis_microarray_02_gsea.Rmd

@@ -278,18 +291,23 @@ The function we will use to map from Ensembl gene IDs to Entrez gene IDs is call
 Let's create a data frame that shows the mapped Entrez IDs along with the differential expression stats for the respective Ensembl IDs.

 ```{r}
-# First let's create a mapped data frame we can join to the differential expression stats
+# First let's create a mapped data frame we can join to the differential


@jashapiro does this section need more info about org.Dr.eg.db per #435 or do you think it's sufficient to link to the more detailed identifier conversion example?

Maybe a little note about where the mapIds() function comes from? Also, in those examples I moved keytype to right after key for "my brain works this way" reasons.

Also, is there a reason entrez_id is in quotes? I don't think we do that elsewhere.

Maybe a little note about where the mapIds() function comes from? Also, in those examples I moved keytype to right after key for "my brain works this way" reasons.

👍

Also, is there a reason entrez_id is in quotes? I don't think we do that elsewhere.

Not that I'm aware of, I can change that.

cbethell

Overall these changes look good to me! (To avoid accidental merging, I won't formally approve just yet as it appears that @jashapiro has a comment or two that have not yet been addressed so consider this an informal approval ✅ )

cbethell · 2020-12-17T14:31:55Z

02-microarray/pathway-analysis_microarray_02_gsea.Rmd

+
+```{r}
+# Set the seed so our results are reproducible:
+set.seed(2020)


We set the seed in the RNA-seq example, but we didn't here. I added a set.seed() step here, right before we "need" it should someone be viewing this example and have jumped to the analysis code. Is this the correct thing to do?

Yes, this is correct. At the time of authoring this example, it was not obvious that the set.seed() step also needed to be added before the GSEA() function, which is why it was left out here. Good point re the placement of the step as well!

jashapiro

This looks good to me. I have a couple citation comments, and otherwise only very minor suggestions.

02-microarray/pathway-analysis_microarray_02_gsea.Rmd

jashapiro · 2020-12-17T15:04:05Z

02-microarray/pathway-analysis_microarray_02_gsea.Rmd


 ```{r}
 msigdbr_species()
 ```

-MSigDB contains 8 different gene set collections [@Subramanian2005].
+MSigDB contains [8 different gene set collections](https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp) [@Subramanian2005] that are distinguished by how they are derived (e.g., computationally mined, curated).


We should probably use the preferred citation here: (Liberzon et al. 2011)

@article{Liberzon2011, doi = {10.1093/bioinformatics/btr260}, url = {https://doi.org/10.1093/bioinformatics/btr260}, year = {2011}, month = may, publisher = {Oxford University Press ({OUP})}, volume = {27}, number = {12}, pages = {1739--1740}, author = {Arthur Liberzon and Aravind Subramanian and Reid Pinchback and Helga Thorvaldsdóttir and Pablo Tamayo and Jill P Mesirov}, title = {Molecular signatures database ({MSigDB}) 3.0}, journal = {Bioinformatics} }

Ah, you mean in addition to @Subramanian2005 correct?

To cite your use of the Molecular Signatures Database (MSigDB), a joint project of UC San Diego and Broad Institute, please reference Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) and one or more of the following as appropriate: Liberzon, et al. (2011, Bionformatics), Liberzon, et al. (2015, Cell Systems), and also the source for the gene set as listed on the gene set page.

Where the 2015 citation is hallmarks, specifically.

Yes, in addition...

👍 I propagated this throughout the pathway analysis notebooks I've gone through so far.

02-microarray/pathway-analysis_microarray_02_gsea.Rmd

Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>

jaclyn-taroni · 2020-12-18T13:24:43Z

When I've run snakemake, I've gotten:

Error in rule render_citations:
    jobid: 9
    output: 02-microarray/pathway-analysis_microarray_01_ora.html
    shell:
        Rscript scripts/render-notebooks.R --rmd 02-microarray/pathway-analysis_microarray_01_ora.Rmd --bib_file components/references.bib --cite_style components/genetics.csl --include_file components/include.R --html 02-microarray/pathway-analysis_microarray_01_ora.html --style
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

But running

Rscript scripts/render-notebooks.R --rmd 03-rnaseq/pathway-analysis_rnaseq_01_ora.Rmd --bib_file components/references.bib --cite_style components/genetics.csl --include_file components/include.R --html 03-rnaseq/pathway-analysis_rnaseq_01_ora.html --style

works fine / no visible error. We should probably figure this out before this get merged, but for the moment I'm going to work on polishing the RNA-seq GSEA notebook.

jashapiro · 2020-12-18T14:11:44Z

I just checked out this branch and ran through everything with

docker run --mount type=bind,target=/home/rstudio,source=$PWD ccdl/refinebio-examples:latest snakemake  --cores 4

I got no errors, so I anticipate that it will work on the server. Should I push the rendered files?

jaclyn-taroni · 2020-12-18T14:13:26Z

These should be up to date rendering wise because I ran the Rscript scripts/render-notebooks.R step but maybe not so sure.

* 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>

jaclyn-taroni added 2 commits December 16, 2020 14:42

Polish wording and add introductory paragraphs

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A bit more polishing

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jaclyn-taroni requested review from jashapiro and cbethell December 16, 2020 20:22

Merge branch 'staging' into jaclyn-taroni/polish-microarray-gsea

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jashapiro reviewed Dec 16, 2020

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jaclyn-taroni and others added 2 commits December 16, 2020 17:24

Apply suggestions from code review

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Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>

Response to code review

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jaclyn-taroni requested a review from jashapiro December 16, 2020 22:57

jashapiro mentioned this pull request Dec 17, 2020

Polish Ensembl Gene ID conversions (bonus reference updates!) #435

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jaclyn-taroni commented Dec 17, 2020

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jashapiro approved these changes Dec 17, 2020

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jaclyn-taroni and others added 4 commits December 17, 2020 17:33

Apply suggestions from code review

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Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>

Propagate citation suggestion to multiple pathway notebooks

b4bf736

Missed these quotes

fe64ea6

A few mapIds() items

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jaclyn-taroni merged commit 0dc67a1 into staging Dec 18, 2020

jaclyn-taroni deleted the jaclyn-taroni/polish-microarray-gsea branch December 18, 2020 14:25

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Polish RNA-seq GSEA example #437

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Add introductory paragraphs to microarray GSEA example, review text for RNA-seq GSEA example #354

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Polish Microarray GSEA example #434

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Polish Microarray GSEA example #434

Polish Microarray GSEA example #434

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