Files in PNNL-Comp-Mass-Spec/RomicsProcessor
omics-oriented package for reproducible and sharable data processing pipelines
.DS_Store
.RData
.Rbuildignore
.Rhistory
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.gitignore
DESCRIPTION
DISCLAIMER.txt
Example/Bacillus_cereus_media_experiment.Rmd
Example/metadata.csv
Example/parameters.txt
Example/proteinGroups.txt
Example/summary.txt
LICENSE.txt
NAMESPACE
R/00_Romics_theme_plots.R
R/01_MaxQuant_Importer.R
R/02_Romics_Base_Functions.R
R/03_CV_calculations.R
R/04_Manage_Missing.R
R/05_Transformation_normalization.R
R/06_Distribution_Plots.R
R/07_Grouping.R
R/08_Heatmap.R
R/09_Statistics.R
R/10_Variable_Plots.R
R/11_sva_Batch_Correction.R
R/12_PmartConvert.R
R/13_Manage_Outliers.R
R/14_Volcano_plot.R
R/15_Trend_analysis.R
R/16_Correlation_plot.R
R/17_featureSubset.R
R/18_Combine_objects.R
R/19_metadata_plots.R
R/Example_data.R
README.md
RomicsProcessor.Rproj
RomicsProcessor_1.1.0.tar.gz
data/.RData
data/.Rapp.history
data/.Rhistory
data/ROP_colors.rdata
data/RomicsProcessor_Example_processed_romics_object.rda
data/RomicsProcessor_Example_romics_data.rda
data/RomicsProcessor_Example_romics_metadata.rda
data/RomicsProcessor_Example_romics_pipeline.rda
data/RomicsProcessor_Example_unprocessed_romics_object.rda
man/Example_processed_romics_object.Rd
man/Example_romics_data.Rd
man/Example_romics_metadata.Rd
man/RomicsBatchCorrection.Rd
man/RomicsCVs.Rd
man/RomicsPmartR.Rd
man/distribBoxplot.Rd
man/distribHistogram.Rd
man/distribHistogramGlobal.Rd
man/distribJitter.Rd
man/distribRidges.Rd
man/distribSina.Rd
man/distribViolin.Rd
man/extractMaxQuant.Rd
man/extractMaxQuantIDs.Rd
man/factorCountLevels.Rd
man/featureSubset.Rd
man/getTrend.Rd
man/imputeMinDiv2.Rd
man/imputeMissing.Rd
man/imputeMissingEval.Rd
man/indPCA3D.Rd
man/indPCAplot.Rd
man/is.romics_object.Rd
man/lmp.Rd
man/log10transform.Rd
man/log2transform.Rd
man/medianCenterSample.Rd
man/medianNormFactor.Rd
man/medianNormSample.Rd
man/metadataRelations.Rd
man/pFrequencyPlot.Rd
man/romicsANOVA.Rd
man/romicsAddDependency.Rd
man/romicsApplyPipeline.Rd
man/romicsCalculatedStats.Rd
man/romicsChangeFactor.Rd
man/romicsChangeIDs.Rd
man/romicsCombineObjects.Rd
man/romicsCorrelation.Rd
man/romicsCreateDependencies.Rd
man/romicsCreateObject.Rd
man/romicsCreatePipeline.Rd
man/romicsDeleteRowMissing.Rd
man/romicsExportData.Rd
man/romicsExtractFactor.Rd
man/romicsFactorNames.Rd
man/romicsFilterMissing.Rd
man/romicsFilterVariable.Rd
man/romicsGlmBinomial.Rd
man/romicsHclust.Rd
man/romicsHeatmap.Rd
man/romicsLogCheck.Rd
man/romicsMean.Rd
man/romicsOutlierEval.Rd
man/romicsOutlierRemove.Rd
man/romicsPCA.Rd
man/romicsPlotMissing.Rd
man/romicsRestoreMissing.Rd
man/romicsSampleNameFromFactor.Rd
man/romicsSd.Rd
man/romicsSteps.Rd
man/romicsSubset.Rd
man/romicsTrend.Rd
man/romicsTrendHeatmap.Rd
man/romicsTtest.Rd
man/romicsUmap.Rd
man/romicsUmapPlot.Rd
man/romicsUpdateColor.Rd
man/romicsUpdateSteps.Rd
man/romicsVariableHclust.Rd
man/romicsVolcano.Rd
man/romicsWilcoxTest.Rd
man/romicsZeroToMissing.Rd
man/romicsZscores.Rd
man/singleVariablePlot.Rd
man/singleVariableTrend.Rd
man/theme_ROP.Rd
man/unlog10data.Rd
man/unlog2data.Rd
test.2022-12-19_13-58-32.log
