From 9a221b23574dedaafaf38055f0665cec1d58321a Mon Sep 17 00:00:00 2001 From: hosseinvk Date: Mon, 10 Aug 2026 13:21:08 +1000 Subject: [PATCH] Move g:Profiler pair back before GSEA/STRING; re-enable Day 1/2 parts Renames 08-1-gprofiler-web.Rmd/08-2-gprofiler2.Rmd -> 06-1/06-2, 06-1-gsea-web.Rmd/06-2-fgsea.Rmd -> 07-1/07-2, and 07-1-string-web.Rmd/07-2-stringdb.Rmd -> 08-1/08-2, restoring g:Profiler (web) + gprofiler2 to immediately follow "Defining the gene list". Content is unchanged except for one stale cross-reference in the gprofiler2-web chapter ("earlier" -> "later in the book", since GSEA now comes after g:Profiler again). Updates make_R_script.R's chapter-exclusion list to match, and reorders the Day 1 schedule on the overview page to follow the new chapter order (durations/instructors unchanged, just resequenced). Also re-adds part-day1.Rmd/part-day2.Rmd into _bookdown.yml's rmd_files (excluded from workshop.R generation, same as other non-code chapters), placed to match the day split used in the overview schedule: Day 1 starts at the Recap chapter, Day 2 starts at clusterProfiler. --- 01-overview.Rmd | 16 ++++++++-------- 08-1-gprofiler-web.Rmd => 06-1-gprofiler-web.Rmd | 2 +- 08-2-gprofiler2.Rmd => 06-2-gprofiler2.Rmd | 0 06-1-gsea-web.Rmd => 07-1-gsea-web.Rmd | 0 06-2-fgsea.Rmd => 07-2-fgsea.Rmd | 0 07-1-string-web.Rmd => 08-1-string-web.Rmd | 0 07-2-stringdb.Rmd => 08-2-stringdb.Rmd | 0 _bookdown.yml | 14 ++++++++------ make_R_script.R | 14 ++++++++------ 9 files changed, 25 insertions(+), 21 deletions(-) rename 08-1-gprofiler-web.Rmd => 06-1-gprofiler-web.Rmd (91%) rename 08-2-gprofiler2.Rmd => 06-2-gprofiler2.Rmd (100%) rename 06-1-gsea-web.Rmd => 07-1-gsea-web.Rmd (100%) rename 06-2-fgsea.Rmd => 07-2-fgsea.Rmd (100%) rename 07-1-string-web.Rmd => 08-1-string-web.Rmd (100%) rename 07-2-stringdb.Rmd => 08-2-stringdb.Rmd (100%) diff --git a/01-overview.Rmd b/01-overview.Rmd index 1c51e47..73e5040 100644 --- a/01-overview.Rmd +++ b/01-overview.Rmd @@ -51,14 +51,14 @@ schedule <- tibble::tibble( rep("HK", 3), # Morning break (10 min) "", + # HK - gProfiler (web) + gprofiler2 + "HK", # GI - GSEA (web) + fgsea "GI", - # GI - STRING (web) + STRINGdb - "GI", # Lunch "", - # HK - gProfiler (web) + gprofiler2 - "HK", + # GI - STRING (web) + STRINGdb + "GI", # SA - Reactome (web) + ReactomePA "SA", # Wrap-up / Q&A / preview Day 2 @@ -70,10 +70,10 @@ schedule <- tibble::tibble( "Data acquisition & filtering gene list", "Interactive Calculator", "Morning break", + "g:Profiler (web) + gprofiler2", "GSEA (web) + fgsea", - "STRING (web) + STRINGdb", "Lunch break", - "g:Profiler (web) + gprofiler2", + "STRING (web) + STRINGdb", "Reactome (web) + ReactomePA", "Wrap-up / Q&A / preview Day 2" ), @@ -81,10 +81,10 @@ schedule <- tibble::tibble( 10, # LP 35, 10, 15, # HK before break 10, # Morning break + 60, # HK: g:Profiler (web) + gprofiler2 60, # GI: GSEA (web) + fgsea - 50, # GI: STRING (web) + STRINGdb 40, # Lunch break - 60, # HK: g:Profiler (web) + gprofiler2 + 50, # GI: STRING (web) + STRINGdb 60, # SA: Reactome (web) + ReactomePA 10 # Wrap-up / Q&A / preview Day 2 ) diff --git a/08-1-gprofiler-web.Rmd b/06-1-gprofiler-web.Rmd similarity index 91% rename from 08-1-gprofiler-web.Rmd rename to 06-1-gprofiler-web.Rmd index 7494f1a..7fcd43d 100644 --- a/08-1-gprofiler-web.Rmd +++ b/06-1-gprofiler-web.Rmd @@ -69,7 +69,7 @@ How can one perform Under Representation Analysis in gProfiler? ### Steps to use a ranked gene list in g:Profiler: -g:Profiler's "Ordered query" option lets you analyse a ranked gene list, but it does **not** implement the Subramanian et al. 2005 GSEA algorithm covered in the GSEA (web) chapter earlier in the book. Instead, it runs standard ORA (hypergeometric/Fisher's exact test) on a series of prefixes of your ranked list (top 10, top 20, top 50 genes, and so on) and reports whichever prefix gives the strongest enrichment for each term. It does not use a running-sum enrichment score, does not weight genes by the magnitude of their ranking metric, and does not use permutation testing — so treat it as ORA over an incrementally-growing ranked list, not as an alternative implementation of GSEA. +g:Profiler's "Ordered query" option lets you analyse a ranked gene list, but it does **not** implement the Subramanian et al. 2005 GSEA algorithm covered in the GSEA (web) chapter later in the book. Instead, it runs standard ORA (hypergeometric/Fisher's exact test) on a series of prefixes of your ranked list (top 10, top 20, top 50 genes, and so on) and reports whichever prefix gives the strongest enrichment for each term. It does not use a running-sum enrichment score, does not weight genes by the magnitude of their ranking metric, and does not use permutation testing — so treat it as ORA over an incrementally-growing ranked list, not as an alternative implementation of GSEA. - Prepare Your Pre-ranked List: Steps to provide a ranked gene list are given [here](degust.html). diff --git a/08-2-gprofiler2.Rmd b/06-2-gprofiler2.Rmd similarity index 100% rename from 08-2-gprofiler2.Rmd rename to 06-2-gprofiler2.Rmd diff --git a/06-1-gsea-web.Rmd b/07-1-gsea-web.Rmd similarity index 100% rename from 06-1-gsea-web.Rmd rename to 07-1-gsea-web.Rmd diff --git a/06-2-fgsea.Rmd b/07-2-fgsea.Rmd similarity index 100% rename from 06-2-fgsea.Rmd rename to 07-2-fgsea.Rmd diff --git a/07-1-string-web.Rmd b/08-1-string-web.Rmd similarity index 100% rename from 07-1-string-web.Rmd rename to 08-1-string-web.Rmd diff --git a/07-2-stringdb.Rmd b/08-2-stringdb.Rmd similarity index 100% rename from 07-2-stringdb.Rmd rename to 08-2-stringdb.Rmd diff --git a/_bookdown.yml b/_bookdown.yml index 2daaa14..f7ad25f 100644 --- a/_bookdown.yml +++ b/_bookdown.yml @@ -10,18 +10,20 @@ rmd_files: - index.Rmd - 01-overview.Rmd - 01-02-setup.Rmd + - part-day1.Rmd - 02-recap.Rmd - 03-stats.Rmd - 04-example-dataset.Rmd - 05-genelists.Rmd - - 06-1-gsea-web.Rmd - - 06-2-fgsea.Rmd - - 07-1-string-web.Rmd - - 07-2-stringdb.Rmd - - 08-1-gprofiler-web.Rmd - - 08-2-gprofiler2.Rmd + - 06-1-gprofiler-web.Rmd + - 06-2-gprofiler2.Rmd + - 07-1-gsea-web.Rmd + - 07-2-fgsea.Rmd + - 08-1-string-web.Rmd + - 08-2-stringdb.Rmd - 09-1-reactome-web.Rmd - 09-2-reactomepa.Rmd + - part-day2.Rmd - 10-clusterprofiler.Rmd - 11-novel-species-FEA.Rmd - 12-uncertainties.Rmd diff --git a/make_R_script.R b/make_R_script.R index fcc201d..89243f3 100644 --- a/make_R_script.R +++ b/make_R_script.R @@ -99,18 +99,20 @@ filenames <- read_yaml("_bookdown.yml", readLines.warn = FALSE)$rmd_files |> "index.Rmd", "01-overview.Rmd", "01-02-setup.Rmd", + "part-day1.Rmd", "02-recap.Rmd", "03-stats.Rmd", "04-example-dataset.Rmd", "05-genelists.Rmd", - "06-1-gsea-web.Rmd", - # "06-2-fgsea.Rmd", - "07-1-string-web.Rmd", - # "07-2-stringdb.Rmd", - "08-1-gprofiler-web.Rmd", - # "08-2-gprofiler2.Rmd", + "06-1-gprofiler-web.Rmd", + # "06-2-gprofiler2.Rmd", + "07-1-gsea-web.Rmd", + # "07-2-fgsea.Rmd", + "08-1-string-web.Rmd", + # "08-2-stringdb.Rmd", "09-1-reactome-web.Rmd", # "09-2-reactomepa.Rmd", + "part-day2.Rmd", # "10-clusterprofiler.Rmd", # "11-novel-species-FEA.Rmd", "12-uncertainties.Rmd",