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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

Name		Name	Last commit message	Last commit date
Latest commit History 73 Commits
.github/workflows		.github/workflows
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
MaxSBM.qmd		MaxSBM.qmd
PTMs.qmd		PTMs.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		changecolumnnames.qmd
changecolumntype.qmd		changecolumntype.qmd
classificationprocessing.qmd		classificationprocessing.qmd
cloneprocessing.qmd		cloneprocessing.qmd
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		combinemaincolumns.qmd
contact.qmd		contact.qmd
convertmultinumeric.qmd		convertmultinumeric.qmd
converttonan.qmd		converttonan.qmd
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		expandmultinumeric.qmd
expandsitetable.qmd		expandsitetable.qmd
fillcategoricalcolumn.qmd		fillcategoricalcolumn.qmd
filtercategoricalcolumn.qmd		filtercategoricalcolumn.qmd
filtercategoricalrow.qmd		filtercategoricalrow.qmd
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

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