Files in cbroeckl/RAMClustR
Mass Spectrometry Metabolomics Feature Clustering and Interpretation
.Rbuildignore
.github/workflows/codecov.yml
.gitignore
CRAN-RELEASE
CRAN-SUBMISSION
ChangeLog
DESCRIPTION
LICENSE
NAMESPACE
R/RCQC.R
R/calculate.similarity.R
R/defineExperiment.R
R/do.findmain.R
R/exportDataset.R
R/findfeature.R
R/findmass.R
R/getData.R
R/mergeRCobjects.R
R/ramclustR.R
R/rc.calibrate.ri.R
R/rc.cmpd.cv.filter.R
R/rc.cmpd.filter.blanks.R
R/rc.cmpd.replace.na.R
R/rc.expand.sample.names.R
R/rc.export.msp.rc.R
R/rc.feature.filter.blanks.R
R/rc.feature.filter.cv.R
R/rc.feature.normalize.batch.qc.R
R/rc.feature.normalize.qc.R
R/rc.feature.normalize.quantile.R
R/rc.feature.normalize.tic.R
R/rc.feature.replace.na.R
R/rc.get.csv.data.R
R/rc.get.df.data.R
R/rc.get.xmcs.data.R
R/rc.merge.clusters.R
R/rc.qc.R
R/rc.ramclustr.R
R/rc.remove.qc.R
R/rc.restore.qc.samples.R
R/write.gcei.mat.R
R/write.methods.R
R/write.msp.R
README.md
conda/environment-dev.yaml
cran-comments.md
docs/ramclustR.png
inst/extdata/featDefinition.rds
inst/extdata/featValues.rds
inst/extdata/peaks.csv
inst/extdata/phenoData.csv
inst/extdata/phenoData_df.rds
inst/params/defparamsets.Rdata
inst/params/greek.csv
inst/params/params.csv
inst/params/paramsets.Rdata
inst/references.txt
man/RCQC.Rd
man/add_params.Rd
man/check_arguments_filter.blanks.Rd
man/check_arguments_filter.cv.Rd
man/check_arguments_replace.na.Rd
man/checks.Rd
man/compute_SpecAbundAve.Rd
man/compute_do.sets.Rd
man/compute_wt_mean.Rd
man/create_ramclustObj.Rd
man/defineExperiment.Rd
man/define_samples.Rd
man/doFindmain.Rd
man/exportDataset.Rd
man/filter_blanks.Rd
man/filter_good_features.Rd
man/filter_signal.Rd
man/find_good_features.Rd
man/findfeature.Rd
man/findmass.Rd
man/getData.Rd
man/get_ExpDes.Rd
man/get_instrument_platform.Rd
man/mean_signal_intensities.Rd
man/mergeRCobjects.Rd
man/normalized_data_batch_qc.Rd
man/normalized_data_tic.Rd
man/order_datasets.Rd
man/ramclustR.Rd
man/rc.calibrate.ri.Rd
man/rc.cmpd.filter.blanks.Rd
man/rc.cmpd.filter.cv.Rd
man/rc.cmpd.replace.na.Rd
man/rc.expand.sample.names.Rd
man/rc.export.msp.rc.Rd
man/rc.feature.filter.blanks.Rd
man/rc.feature.filter.cv.Rd
man/rc.feature.normalize.batch.qc.Rd
man/rc.feature.normalize.qc.Rd
man/rc.feature.normalize.quantile.Rd
man/rc.feature.normalize.tic.Rd
man/rc.feature.replace.na.Rd
man/rc.get.csv.data.Rd
man/rc.get.df.data.Rd
man/rc.get.xcms.data.Rd
man/rc.merge.split.clusters.Rd
man/rc.qc.Rd
man/rc.ramclustr.Rd
man/rc.remove.qc.Rd
man/rc.restore.qc.samples.Rd
man/remove_blanks.Rd
man/replace_na.Rd
man/write.gcei.mat.Rd
man/write.methods.Rd
man/write.msp.Rd
man/write_csv.Rd
tests/testthat.R
tests/testthat/helper.R
tests/testthat/test-do.findmain.R
tests/testthat/test-rc.calibrate.ri.R
tests/testthat/test-rc.expand.sample.names.R
tests/testthat/test-rc.feature.filter.blanks.R
tests/testthat/test-rc.feature.filter.cv.R
tests/testthat/test-rc.feature.normalize.qc.R
tests/testthat/test-rc.feature.replace.na.R
tests/testthat/test-rc.get.csv.data.R
tests/testthat/test-rc.get.df.data.R
tests/testthat/test-rc.get.xcms.data.R
tests/testthat/test-rc.qc.R
tests/testthat/test-rc.ramclustr.R
tests/testthat/test-rc.remove.qc.R
tests/testthat/test-rc.restore.qc.samples.R
tests/testthat/test-stepwise-workflow.R
tests/testthat/test-workflow-comparison.R
tests/testthat/test.R
tests/testthat/testdata/calibrant.data.csv
tests/testthat/testdata/clustering/normal_rc.ramclustr.rds
tests/testthat/testdata/clustering/only_rt_rc.ramclustr.rds
tests/testthat/testdata/do.findmain.rds
tests/testthat/testdata/input.rc.calibrate.ri.rds
tests/testthat/testdata/ms1_featureDefinitions.rds
tests/testthat/testdata/ms1_featureValues.rds
tests/testthat/testdata/output.msp
tests/testthat/testdata/peaks.csv
tests/testthat/testdata/phenoData.csv
tests/testthat/testdata/phenoData_df.rds
tests/testthat/testdata/rc.calibrate.ri.rds
tests/testthat/testdata/rc.expand.sample.names.rds
tests/testthat/testdata/rc.feature.filter.blanks.rds
tests/testthat/testdata/rc.feature.filter.cv.rds
tests/testthat/testdata/rc.feature.normalize.qc.rds
tests/testthat/testdata/rc.feature.replace.na.rds
tests/testthat/testdata/rc.get.csv.data.rds
tests/testthat/testdata/rc.get.df.data.rds
tests/testthat/testdata/rc.get.xcms.data.rds
tests/testthat/testdata/rc.qc.rds
tests/testthat/testdata/rc.remove.qc.rds
tests/testthat/testdata/rc.restore.qc.samples.rds
tests/testthat/testdata/test.fillpeaks
tests/testthat/testdata/test_csv.rds
vignettes/ExpDes.csv
vignettes/RAMClustR.Rmd
vignettes/spectra/test.mspLib
