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.github/workflows
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Figures
Figures
 
 
_extensions
_extensions
 
 
backup
backup
 
 
docs
docs
 
 
images
images
 
 
.gitignore
.gitignore
 
 
.nojekyll
.nojekyll
 
 
ClassificationFeatureSelection.qmd
ClassificationFeatureSelection.qmd
 
 
ClassificationParameterOptimization.qmd
ClassificationParameterOptimization.qmd
 
 
ClusterNorm.qmd
ClusterNorm.qmd
 
 
Download_Installation.ipynb
Download_Installation.ipynb
 
 
Download_Installation.qmd
Download_Installation.qmd
 
 
Glossary.qmd
Glossary.qmd
 
 
Install_dotnet.sh
Install_dotnet.sh
 
 
MQ_FirstSteps.qmd
MQ_FirstSteps.qmd
 
 
README.md
README.md
 
 
WGCNA.qmd
WGCNA.qmd
 
 
_quarto.yml
_quarto.yml
 
 
addannotationtomatrix.qmd
addannotationtomatrix.qmd
 
 
addknownsites.qmd
addknownsites.qmd
 
 
addlinearmotifs.qmd
addlinearmotifs.qmd
 
 
addmodificationcounts.qmd
addmodificationcounts.qmd
 
 
addnoise.qmd
addnoise.qmd
 
 
addregulatorysites.qmd
addregulatorysites.qmd
 
 
addsequencefeatures.qmd
addsequencefeatures.qmd
 
 
andromeda_configurations.qmd
andromeda_configurations.qmd
 
 
andromeda_enzymes.qmd
andromeda_enzymes.qmd
 
 
andromeda_instructions.qmd
andromeda_instructions.qmd
 
 
andromeda_modifications_table.qmd
andromeda_modifications_table.qmd
 
 
andromeda_protdatabases.qmd
andromeda_protdatabases.qmd
 
 
andromeda_tutorial.qmd
andromeda_tutorial.qmd
 
 
andromeda_user-interface.qmd
andromeda_user-interface.qmd
 
 
annotateproteins.qmd
annotateproteins.qmd
 
 
assertmatrixequal.qmd
assertmatrixequal.qmd
 
 
averagecategories.qmd
averagecategories.qmd
 
 
averagegroups.qmd
averagegroups.qmd
 
 
backtobaseidentifiers.qmd
backtobaseidentifiers.qmd
 
 
binaryupload.qmd
binaryupload.qmd
 
 
categorycounting.qmd
categorycounting.qmd
 
 
changecolumnnames.qmd
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changecolumntype.qmd
changecolumntype.qmd
 
 
classificationprocessing.qmd
classificationprocessing.qmd
 
 
cloneprocessing.qmd
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coexpressionclustering.qmd
coexpressionclustering.qmd
 
 
columncorrelations.qmd
columncorrelations.qmd
 
 
combineannotations.qmd
combineannotations.qmd
 
 
combinebyidentifiersprocessing.qmd
combinebyidentifiersprocessing.qmd
 
 
combinecategoricalcolumns.qmd
combinecategoricalcolumns.qmd
 
 
combineexpressioncolumns.qmd
combineexpressioncolumns.qmd
 
 
combinemaincolumns.qmd
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contact.qmd
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convertmultinumeric.qmd
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converttonan.qmd
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correlate.qmd
correlate.qmd
 
 
coxdocs.CoxLab.Rproj
coxdocs.CoxLab.Rproj
 
 
createcategoricalannotrow.qmd
createcategoricalannotrow.qmd
 
 
creategenelist.qmd
creategenelist.qmd
 
 
createnumericalannotrow.qmd
createnumericalannotrow.qmd
 
 
createqualitymatrix.qmd
createqualitymatrix.qmd
 
 
createrandommatrix.qmd
createrandommatrix.qmd
 
 
cyclicannotation.qmd
cyclicannotation.qmd
 
 
dehyphenateids.qmd
dehyphenateids.qmd
 
 
densityestimationprocessing.qmd
densityestimationprocessing.qmd
 
 
developersguide.qmd
developersguide.qmd
 
 
divide.qmd
divide.qmd
 
 
duplicatecolumns.qmd
duplicatecolumns.qmd
 
 
estimateaccuracy.qmd
estimateaccuracy.qmd
 
 
estimatecopynumbers.qmd
estimatecopynumbers.qmd
 
 
expandmultinumeric.qmd
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expandsitetable.qmd
expandsitetable.qmd
 
 
fillcategoricalcolumn.qmd
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filtercategoricalrow.qmd
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filternumericalcolumn.qmd
filternumericalcolumn.qmd
 
 
filterquality.qmd
filterquality.qmd
 
 
filterrandomrows.qmd
filterrandomrows.qmd
 
 
filtertextualcolumn.qmd
filtertextualcolumn.qmd
 
 
filtervalidvaluescolumns.qmd
filtervalidvaluescolumns.qmd
 
 
filtervalidvaluesrows.qmd
filtervalidvaluesrows.qmd
 
 
fisherexacttestproces.qmd
fisherexacttestproces.qmd
 
 
genericclusteringproc.qmd
genericclusteringproc.qmd
 
 
genericmatrixupload.qmd
genericmatrixupload.qmd
 
 
hawaiiplot.qmd
hawaiiplot.qmd
 
 
hierarchicalcluster.qmd
hierarchicalcluster.qmd
 
 
histogram.qmd
histogram.qmd
 
 
htseqvsperseus.table.rar
htseqvsperseus.table.rar
 
 
index.qmd
index.qmd
 
 
interactions.qmd
interactions.qmd
 
 
jointermsincategoricalrow.qmd
jointermsincategoricalrow.qmd
 
 
kinasesubstraterelations.qmd
kinasesubstraterelations.qmd
 
 
managecategoricalannotrow.qmd
managecategoricalannotrow.qmd
 
 
managenumericalannotrow.qmd
managenumericalannotrow.qmd
 
 
matchingcolumnsbyname.qmd
matchingcolumnsbyname.qmd
 
 
matchingrowsbyname.qmd
matchingrowsbyname.qmd
 
 
maxquant_instructions.qmd
maxquant_instructions.qmd
 
 
modifications.qmd
modifications.qmd
 
 
multiplesampletestprocessing.qmd
multiplesampletestprocessing.qmd
 
 
multiscatteranalysis.qmd
multiscatteranalysis.qmd
 
 
nature.csl
nature.csl
 
 

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Cox Docs

Instructions how to use MaxQuant and Perseus for the analysis of Proteomics data

the page was created using Quarto and RStudio and is hosted on github

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