links updated

the "docs/ " prefix was removed from all paths.
cox-labs · Nov 15, 2023 · 0d118df · 0d118df
1 parent 1ae3ba7
commit 0d118df
Show file tree

Hide file tree

Showing 468 changed files with 102,539 additions and 944 deletions.
diff --git a/WGCNA.qmd b/WGCNA.qmd
@@ -49,5 +49,5 @@ You are now ready to perform co-expression analysis from within Perseus.
 
 ## WGCNA functions
 
-* [Soft-threshold](docs/softthreshold.html)
-* [Co-expression clustering](docs/coexpressionclustering.html)
+* [Soft-threshold](softthreshold.html)
+* [Co-expression clustering](coexpressionclustering.html)
diff --git a/annotateproteins.qmd b/annotateproteins.qmd
@@ -15,9 +15,9 @@ csl: nature.csl
 ---
 
 
-If you arrived here directly from Perseus, it is a good idea to read the [Proteomic ruler overview](docs/proteomicruler.html) first.
+If you arrived here directly from Perseus, it is a good idea to read the [Proteomic ruler overview](proteomicruler.html) first.
 
-For those that want to apply the proteomic ruler concept and are in a hurry: If you imported the columns _Sequence length_ and _Molecular weight_ of your proteinGroups.txt, you can skip this and directly [estimate copy numbers](docs/estimatecopynumbers.html).
+For those that want to apply the proteomic ruler concept and are in a hurry: If you imported the columns _Sequence length_ and _Molecular weight_ of your proteinGroups.txt, you can skip this and directly [estimate copy numbers](estimatecopynumbers.html).
 
 # Description
 
@@ -33,7 +33,7 @@ extracts information from the UniProt fasta file that was used to process a data
 # Parameters
 
 Most of the parameters should be self-explanatory. Hover the mouse over the descriptions to get detailed help.
-The Plugin will pre-select the most useful parameters and auto-detect the correct input columns (if present in your matrix). These default parameters will cover everything needed to [estimate copy numbers](docs/estimatecopynumbers.html).
+The Plugin will pre-select the most useful parameters and auto-detect the correct input columns (if present in your matrix). These default parameters will cover everything needed to [estimate copy numbers](estimatecopynumbers.html).
 
 ## Input
 

diff --git a/backtobaseidentifiers.qmd b/backtobaseidentifiers.qmd
@@ -21,7 +21,7 @@ bibliography: references.bib
 
 # Brief description
 
-This activity does the inverse of the [Add annotation](docs/addannotationtomatrix.html) activity. Any of the columns that can be created by the [Add annotation](docs/addannotationtomatrix.html) activity can be mapped back to the base identifiers (typically UniProt ids).
+This activity does the inverse of the [Add annotation](addannotationtomatrix.html) activity. Any of the columns that can be created by the [Add annotation](addannotationtomatrix.html) activity can be mapped back to the base identifiers (typically UniProt ids).
 
 ```{=html}
 <!-- This comment and the line above it must be preserved when editing this file!

diff --git a/.../docs/ClassificationFeatureSelection.html → backup/ClassificationFeatureSelection.html b/.../docs/ClassificationFeatureSelection.html → backup/ClassificationFeatureSelection.html
diff --git a/.../ClassificationParameterOptimization.html → .../ClassificationParameterOptimization.html b/.../ClassificationParameterOptimization.html → .../ClassificationParameterOptimization.html
diff --git a/docs/docs/ClusterNorm.html → backup/ClusterNorm.html b/docs/docs/ClusterNorm.html → backup/ClusterNorm.html
diff --git a/backup/Download_Installation.html b/backup/Download_Installation.html
diff --git a/docs/docs/Glossary.html → backup/Glossary.html b/docs/docs/Glossary.html → backup/Glossary.html
diff --git a/backup/MQ_FirstSteps.html b/backup/MQ_FirstSteps.html
diff --git a/docs/docs/WGCNA.html → backup/WGCNA.html b/docs/docs/WGCNA.html → backup/WGCNA.html
diff --git a/docs/docs/addannotationtomatrix.html → backup/addannotationtomatrix.html b/docs/docs/addannotationtomatrix.html → backup/addannotationtomatrix.html
diff --git a/docs/docs/addknownsites.html → backup/addknownsites.html b/docs/docs/addknownsites.html → backup/addknownsites.html
diff --git a/docs/docs/addlinearmotifs.html → backup/addlinearmotifs.html b/docs/docs/addlinearmotifs.html → backup/addlinearmotifs.html
diff --git a/docs/docs/addmodificationcounts.html → backup/addmodificationcounts.html b/docs/docs/addmodificationcounts.html → backup/addmodificationcounts.html
diff --git a/docs/docs/addnoise.html → backup/addnoise.html b/docs/docs/addnoise.html → backup/addnoise.html
diff --git a/docs/docs/addregulatorysites.html → backup/addregulatorysites.html b/docs/docs/addregulatorysites.html → backup/addregulatorysites.html
diff --git a/docs/docs/addsequencefeatures.html → backup/addsequencefeatures.html b/docs/docs/addsequencefeatures.html → backup/addsequencefeatures.html