Files in pmartR/pmartR
Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check-examples.yaml
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
DISCLAIMER.md
LICENSE
LICENSE.md
NAMESPACE
R/MSnSet2pepData.R
R/RcppExports.R
R/applyFilt.R
R/as.multiData.R
R/as.omicsData.R
R/as.trelliData.R
R/bpquant.R
R/combine_lipidData.R
R/combine_techreps.R
R/cor_result.R
R/custom_sampnames.R
R/dim_reduction.R
R/dopar.R
R/edata_replace.R
R/edata_summary.R
R/edata_transform.R
R/filter_objects.R
R/filter_summary.R
R/get_comparisons.R
R/group_designation.R
R/helper_fn.R
R/imd_anova.R
R/missingval_result.R
R/nonmissing_per_group.R
R/normRes_tests.R
R/norm_funcs.R
R/normalize_global.R
R/normalize_isobaric.R
R/normalize_loess.R
R/normalize_nmr.R
R/normalize_quantile.R
R/pipe.R
R/plot_fns.R
R/pmartR.R
R/pre_imdanova_melt.R
R/print_data_objects.R
R/print_filter_objects.R
R/protein_quant.R
R/report_dataRes.R
R/results_summary.R
R/rmd_conversion.R
R/seqData_wrappers.R
R/spans.R
R/statRes_class.R
R/subset_funcs.R
R/summary_isobaricnormRes.R
R/summary_nmrnormRes.R
R/summary_pmartR.R
R/summary_trelliData.R
R/surv_designation.R
R/survival.R
R/trelliPlots.R
R/trelliPlots_seqData.R
README.md
_pkgdown.yml
cran-comments.md
inst/CITATION
inst/testdata/imd_anova_standard_fns.R
inst/testdata/lipidData.R
inst/testdata/lipidData.RData
inst/testdata/little_isodata.R
inst/testdata/little_isodata.RData
inst/testdata/little_pairdata.R
inst/testdata/little_pairdata.RData
inst/testdata/little_pdata.R
inst/testdata/little_pdata.RData
inst/testdata/little_prdata.R
inst/testdata/little_prdata.RData
inst/testdata/little_seqdata.RData
inst/testdata/little_techdata.R
inst/testdata/little_techdata.RData
inst/testdata/load_data.R
inst/testdata/metaboliteData.R
inst/testdata/metaboliteData.RData
inst/testdata/nmrData.R
inst/testdata/nmrData.RData
inst/testdata/plot_objects.R
inst/testdata/plot_objects.RData
inst/testdata/sour_grapes.csv
inst/testdata/sour_grapes_2.csv
inst/testdata/standard_imd_anova_paired.R
inst/testdata/standards_filter.RData
inst/testdata/standards_filter_paired.RData
inst/testdata/standards_imd_anova.R
inst/testdata/standards_imd_anova.RData
inst/testdata/standards_imd_anova_paired.RData
man/DESeq2_wrapper.Rd
man/RNA_filter.Rd
man/all_subset.Rd
man/anova_filter.Rd
man/anova_test.Rd
man/applyFilt.Rd
man/as.isobaricpepData.Rd
man/as.lipidData.Rd
man/as.metabData.Rd
man/as.multiData.Rd
man/as.nmrData.Rd
man/as.pepData.Rd
man/as.proData.Rd
man/as.seqData.Rd
man/as.trelliData.Rd
man/as.trelliData.edata.Rd
man/bpquant.Rd
man/bpquant_mod.Rd
man/column_matches_exact.Rd
man/combine_lipidData.Rd
man/combine_techreps.Rd
man/complete_mols.Rd
man/cor_result.Rd
man/create_comparisonDF.Rd
man/custom_filter.Rd
man/custom_sampnames.Rd
man/cv_filter.Rd
man/diffexp_seq.Rd
man/dim_reduction.Rd
man/dispersion_est.Rd
man/dot-is_edata.Rd
man/edata_replace.Rd
man/edata_summary.Rd
man/edata_transform.Rd
man/edgeR_wrapper.Rd
man/find_fmeta_cnames.Rd
man/fit_surv.Rd
man/fmeta_matches.Rd
man/get_check_names.Rd
man/get_comparisons.Rd
man/get_data_class.Rd
man/get_data_info.Rd
man/get_data_norm.Rd
man/get_data_scale.Rd
man/get_data_scale_orig.Rd
man/get_edata_cname.Rd
man/get_emeta_cname.Rd
man/get_fdata_cname.Rd
man/get_filter_type.Rd
man/get_filters.Rd
man/get_group_DF.Rd
man/get_group_formula.Rd
man/get_group_table.Rd
man/get_isobaric_info.Rd
man/get_isobaric_norm.Rd
man/get_lsmeans.Rd
man/get_meta_info.Rd
man/get_nmr_info.Rd
man/get_nmr_norm.Rd
man/get_pred_grid.Rd
man/get_spans_params.Rd
man/group_comparison_anova.Rd
man/group_comparison_imd.Rd
man/group_designation.Rd
man/gtest_filter.Rd
man/gtest_heatmap.Rd
man/imd_anova.Rd
man/imd_test.Rd
man/imdanova_filter.Rd
man/los.Rd
man/mad_transform.Rd
man/make_volcano_plot_df.Rd
man/mean_center.Rd
man/median_center.Rd
man/missingval_result.Rd
man/molecule_filter.Rd
man/nonmissing_per_group.Rd
man/normRes_tests.Rd
man/normalize_global.Rd
man/normalize_global_basic.Rd
man/normalize_isobaric.Rd
man/normalize_loess.Rd
man/normalize_nmr.Rd
man/normalize_quantile.Rd
man/p_adjustment_anova.Rd
man/plot-RNAFilt.Rd
man/plot-SPANSRes.Rd
man/plot-corRes.Rd
man/plot-customFilt.Rd
man/plot-cvFilt.Rd
man/plot-dataRes.Rd
man/plot-dimRes.Rd
man/plot-imdanovaFilt.Rd
man/plot-isobaricnormRes.Rd
man/plot-isobaricpepData.Rd
man/plot-lipidData.Rd
man/plot-metabData.Rd
man/plot-moleculeFilt.Rd
man/plot-naRes.Rd
man/plot-nmrData.Rd
man/plot-nmrnormRes.Rd
man/plot-normRes.Rd
man/plot-pepData.Rd
man/plot-proData.Rd
man/plot-proteomicsFilt.Rd
man/plot-rmdFilt.Rd
man/plot-seqData.Rd
man/plot-totalCountFilt.Rd
man/plot.statRes.Rd
man/plot_km.Rd
man/pmartR.Rd
man/pmartR_filter_worker.Rd
man/ppp.Rd
man/ppp_rip.Rd
man/pquant.Rd
man/pre_imdanova_melt.Rd
man/prep_flags.Rd
man/print-RNAFilt.Rd
man/print-customFilt.Rd
man/print-cvFilt.Rd
man/print-dataRes.Rd
man/print-imdanovaFilt.Rd
man/print-lipidData.Rd
man/print-metabData.Rd
man/print-moleculeFilt.Rd
man/print-normRes.Rd
man/print-pepData.Rd
man/print-proData.Rd
man/print-proteomicsFilt.Rd
man/print-rmdFilt.Rd
man/print-seqData.Rd
man/print-totalCountFilt.Rd
man/print.RNAFiltSummary.Rd
man/print.customFilterSummary.Rd
man/print.cvFilterSummary.Rd
man/print.imdanovaFilterSummary.Rd
man/print.moleculeFilterSummary.Rd
man/print.proteomicsFilterSummary.Rd
man/print.rmdFilterSummary.Rd
man/print.totalCountFiltSummary.Rd
man/protein_quant.Rd
man/proteomics_filter.Rd
man/qrollup.Rd
man/reexports.Rd
man/replace_nas.Rd
man/replace_zeros.Rd
man/report_dataRes.Rd
man/rip.Rd
man/rmd_conversion.Rd
man/rmd_filter.Rd
man/rrollup.Rd
man/run_group_meancor.Rd
man/run_kurtosis.Rd
man/run_mad.Rd
man/run_prop_missing.Rd
man/run_skewness.Rd
man/set_check_names.Rd
man/set_data_info.Rd
man/set_filter.Rd
man/set_isobaric_info.Rd
man/set_meta_info.Rd
man/set_nmr_info.Rd
man/spans_make_distribution.Rd
man/spans_procedure.Rd
man/statRes-class.Rd
man/statRes_output.Rd
man/statres_barplot.Rd
man/statres_volcano_plot.Rd
man/summary-isobaricnormRes.Rd
man/summary-nmrnormRes.Rd
man/summary-omicsData.Rd
man/summary-pmartR-results.Rd
man/summary-trelliData.Rd
man/summary.RNAFilt.Rd
man/summary.customFilt.Rd
man/summary.cvFilt.Rd
man/summary.imdanovaFilt.Rd
man/summary.moleculeFilt.Rd
man/summary.proteomicsFilt.Rd
man/summary.rmdFilt.Rd
man/summary.totalCountFilt.Rd
man/summary_km.Rd
man/surv_designation.Rd
man/take_diff.Rd
man/total_count_filter.Rd
man/trelli_abundance_boxplot.Rd
man/trelli_abundance_heatmap.Rd
man/trelli_abundance_histogram.Rd
man/trelli_foldchange_bar.Rd
man/trelli_foldchange_boxplot.Rd
man/trelli_foldchange_heatmap.Rd
man/trelli_foldchange_volcano.Rd
man/trelli_missingness_bar.Rd
man/trelli_panel_by.Rd
man/trelli_precheck.Rd
man/trelli_pvalue_filter.Rd
man/trelli_rnaseq_boxplot.Rd
man/trelli_rnaseq_heatmap.Rd
man/trelli_rnaseq_histogram.Rd
man/trelli_rnaseq_nonzero_bar.Rd
man/vector_replace.Rd
man/voom_wrapper.Rd
man/zrollup.Rd
man/zscore_transform.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/calculate_cv.cpp
src/count_missing_cpp.cpp
src/imd_anova.cpp
src/kw_rcpp.cpp
src/nonmissing_per_grp.cpp
tests/testthat.R
tests/testthat/_snaps/plots/plot-corres.svg
tests/testthat/_snaps/plots/plot-cvfilt-log-scale.svg
tests/testthat/_snaps/plots/plot-cvfilt.svg
tests/testthat/_snaps/plots/plot-datares-bw-theme.svg
tests/testthat/_snaps/plots/plot-datares-palette.svg
tests/testthat/_snaps/plots/plot-datares.svg
tests/testthat/_snaps/plots/plot-dimres.svg
tests/testthat/_snaps/plots/plot-imdanovafilt.svg
tests/testthat/_snaps/plots/plot-isobaricnormres-bw-theme.svg
tests/testthat/_snaps/plots/plot-isobaricnormres-global-normalized.svg
tests/testthat/_snaps/plots/plot-isobaricnormres-palette.svg
tests/testthat/_snaps/plots/plot-isobaricnormres.svg
tests/testthat/_snaps/plots/plot-isobaricpepdata.svg
tests/testthat/_snaps/plots/plot-lipiddata.svg
tests/testthat/_snaps/plots/plot-metabdata.svg
tests/testthat/_snaps/plots/plot-moleculefilt-cumulative.svg
tests/testthat/_snaps/plots/plot-moleculefilt.svg
tests/testthat/_snaps/plots/plot-nares-bar-group-color.svg
tests/testthat/_snaps/plots/plot-nares-bar-group-order.svg
tests/testthat/_snaps/plots/plot-nares-scatter.svg
tests/testthat/_snaps/plots/plot-nmrdata.svg
tests/testthat/_snaps/plots/plot-nmrnormres-2.svg
tests/testthat/_snaps/plots/plot-nmrnormres-color-by.svg
tests/testthat/_snaps/plots/plot-nmrnormres.svg
tests/testthat/_snaps/plots/plot-normres.svg
tests/testthat/_snaps/plots/plot-pepdata.svg
tests/testthat/_snaps/plots/plot-prodata.svg
tests/testthat/_snaps/plots/plot-proteomicsfilt-redundancy.svg
tests/testthat/_snaps/plots/plot-proteomicsfilt.svg
tests/testthat/_snaps/plots/plot-rmdfilt.svg
tests/testthat/_snaps/plots/plot-rnafilt.svg
tests/testthat/_snaps/plots/plot-seqdata.svg
tests/testthat/_snaps/plots/plot-spansres-bw-theme.svg
tests/testthat/_snaps/plots/plot-spansres-color-high-color-low.svg
tests/testthat/_snaps/plots/plot-spansres.svg
tests/testthat/_snaps/plots/plot-statres-anova-volcano.svg
tests/testthat/_snaps/plots/plot-statres-anova.svg
tests/testthat/_snaps/plots/plot-statres-combined-volcano.svg
tests/testthat/_snaps/plots/plot-statres-combined.svg
tests/testthat/_snaps/plots/plot-statres-gtest.svg
tests/testthat/_snaps/plots/plot-totalcountfilt.svg
tests/testthat/images/placeholder.txt
tests/testthat/test_as_isobaricpepData.R
tests/testthat/test_as_lipidData.R
tests/testthat/test_as_metabData.R
tests/testthat/test_as_multiData.R
tests/testthat/test_as_nmrData.R
tests/testthat/test_as_pepData.R
tests/testthat/test_as_proData.R
tests/testthat/test_as_seqData.R
tests/testthat/test_as_trelliData.R
tests/testthat/test_as_trelliData_edata.R
tests/testthat/test_as_trelliData_summary.R
tests/testthat/test_combine_omicsData.R
tests/testthat/test_combine_techreps.R
tests/testthat/test_custom_sampnames.R
tests/testthat/test_diffexp_seq.R
tests/testthat/test_dim_reduction.R
tests/testthat/test_dispersion_est.R
tests/testthat/test_edata_replace.R
tests/testthat/test_edata_structure.R
tests/testthat/test_edata_summary.R
tests/testthat/test_edata_transform.R
tests/testthat/test_filter_RNA.R
tests/testthat/test_filter_custom.R
tests/testthat/test_filter_cv.R
tests/testthat/test_filter_imdanova.R
tests/testthat/test_filter_molecule.R
tests/testthat/test_filter_proteomics.R
tests/testthat/test_filter_rmd.R
tests/testthat/test_filter_total_count.R
tests/testthat/test_get_group_formula.R
tests/testthat/test_group_designation.R
tests/testthat/test_helper_fns.R
tests/testthat/test_imd_anova.R
tests/testthat/test_imd_anova_paired.R
tests/testthat/test_imdanova_helpers.R
tests/testthat/test_kw_rcpp.R
tests/testthat/test_nonmissing_per_grp.R
tests/testthat/test_normRes_tests.R
tests/testthat/test_normalize_global.R
tests/testthat/test_normalize_isobaric.R
tests/testthat/test_normalize_nmr.R
tests/testthat/test_normalize_quantile.R
tests/testthat/test_normalize_spans.R
tests/testthat/test_plot_errors.R
tests/testthat/test_plots.R
tests/testthat/test_pooled_cv_rcpp.R
tests/testthat/test_quant_bp.R
tests/testthat/test_quant_protein.R
tests/testthat/test_replace_zeros.R
tests/testthat/test_result_cor.R
tests/testthat/test_result_missingval.R
tests/testthat/test_rmd_conversion.R
tests/testthat/test_summary_filter.R
tests/testthat/test_summary_omicsData.R
tests/testthat/test_trelliPlots.R
tests/testthat/test_trelliPlots_seqData.R
tests/testthat/test_trelli_pvalue_filter.R
vignettes/Convenience_Functions.Rmd
vignettes/Data_Normalization.Rmd
vignettes/Data_Object_Creation.Rmd
vignettes/Filter_Functionality.Rmd
vignettes/Graphing_with_pmartR.Rmd
vignettes/RNAseq_Data_Processing.R
vignettes/RNAseq_Processing_Workflow.Rmd
vignettes/SPANS_isobaricpep.png
vignettes/SPANS_pep.png
vignettes/Statistical_Analysis_with_pmartR.Rmd
vignettes/TrelliData_Plotting_Options.png
vignettes/Trelliscope_Vignette.Rmd
vignettes/Typical_Processing_Workflow.Rmd
vignettes/WorkflowFigure.png
vignettes/bibliography.bib
vignettes/modify_mathjax.html
vignettes/pmartR_graphic-final.jpg
vignettes/pmartR_logo_final.jpg
vignettes/pmartRstat_lit.bib
vignettes/spans_result.RDS
