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pmartR  

Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data
View on CRAN: Click here


Download and install pmartR package within the R console
Install from CRAN:
install.packages("pmartR")

Install from Github:
library("remotes")
install_github("cran/pmartR")

Install by package version:
library("remotes")
install_version("pmartR", "2.5.1")



Attach the package and use:
library("pmartR")
Maintained by
Lisa Bramer
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-12-06
Latest Update: 2025-04-23
Description:
Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) . Webb-Robertson et al. (2011) . Matzke et al. (2011) . Matzke et al. (2013) . Polpitiya et al. (2008) . Webb-Robertson et al. (2010) .
How to cite:
Lisa Bramer (2023). pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data. R package version 2.5.1, https://cran.r-project.org/web/packages/pmartR. Accessed 05 Jun. 2026.
Previous versions and publish date:
2.4.1 (2023-12-06 11:30), 2.4.2 (2023-12-12 11:50), 2.4.3 (2024-02-27 00:50), 2.4.4 (2024-02-27 22:20), 2.4.5 (2024-05-21 17:50), 2.4.6 (2024-10-14 23:10), 2.5.0 (2025-04-23 20:00)
Other packages that cited pmartR R package
View pmartR citation profile
Other R packages that pmartR depends, imports, suggests or enhances
Complete documentation for pmartR
Functions, R codes and Examples using the pmartR R package
Some associated functions: DESeq2_wrapper . RNA_filter . all_subset . anova_filter . anova_test . applyFilt . as.isobaricpepData . as.lipidData . as.metabData . as.multiData . as.nmrData . as.pepData . as.proData . as.seqData . as.trelliData.edata . as.trelliData . bpquant . bpquant_mod . column_matches_exact . combine_lipidData . combine_techreps . complete_mols . cor_result . create_comparisonDF . custom_filter . custom_sampnames . cv_filter . diffexp_seq . dim_reduction . dispersion_est . dot-is_edata . edata_replace . edata_summary . edata_transform . edgeR_wrapper . find_fmeta_cnames . fit_surv . fmeta_matches . get_check_names . get_comparisons . get_data_class . get_data_info . get_data_norm . get_data_scale . get_data_scale_orig . get_edata_cname . get_emeta_cname . get_fdata_cname . get_filter_type . get_filters . get_group_DF . get_group_formula . get_group_table . get_isobaric_info . get_isobaric_norm . get_lsmeans . get_meta_info . get_nmr_info . get_nmr_norm . get_pred_grid . get_spans_params . group_comparison_anova . group_comparison_imd . group_designation . gtest_filter . gtest_heatmap . imd_anova . imd_test . imdanova_filter . los . mad_transform . make_volcano_plot_df . mean_center . median_center . missingval_result . molecule_filter . nonmissing_per_group . normRes_tests . normalize_global . normalize_global_basic . normalize_isobaric . normalize_loess . normalize_nmr . normalize_quantile . p_adjustment_anova . plot-RNAFilt . plot-SPANSRes . plot-corRes . plot-customFilt . plot-cvFilt . plot-dataRes . plot-dimRes . plot-imdanovaFilt . plot-isobaricnormRes . plot-isobaricpepData . plot-lipidData . plot-metabData . plot-moleculeFilt . plot-naRes . plot-nmrData . plot-nmrnormRes . plot-normRes . plot-pepData . plot-proData . plot-proteomicsFilt . plot-rmdFilt . plot-seqData . plot-totalCountFilt . plot.statRes . plot_km . pmartR . pmartR_filter_worker . ppp . ppp_rip . pquant . pre_imdanova_melt . prep_flags . print-RNAFilt . print-customFilt . print-cvFilt . print-dataRes . print-imdanovaFilt . print-lipidData . print-metabData . print-moleculeFilt . print-normRes . print-pepData . print-proData . print-proteomicsFilt . print-rmdFilt . print-seqData . print-totalCountFilt . print.RNAFiltSummary . print.customFilterSummary . print.cvFilterSummary . print.imdanovaFilterSummary . print.moleculeFilterSummary . print.proteomicsFilterSummary . print.rmdFilterSummary . print.totalCountFiltSummary . protein_quant . proteomics_filter . qrollup . reexports . replace_nas . replace_zeros . report_dataRes . rip . rmd_conversion . rmd_filter . rrollup . run_group_meancor . run_kurtosis . run_mad . run_prop_missing . run_skewness . set_check_names . set_data_info . set_filter . set_isobaric_info . set_meta_info . set_nmr_info . spans_make_distribution . spans_procedure . statRes-class . statRes_output . statres_barplot . statres_volcano_plot . summary-isobaricnormRes . summary-nmrnormRes . summary-omicsData . summary-pmartR-results . summary-trelliData . summary.RNAFilt . summary.customFilt . summary.cvFilt . summary.imdanovaFilt . summary.moleculeFilt . summary.proteomicsFilt . summary.rmdFilt . summary.totalCountFilt . summary_km . surv_designation . take_diff . total_count_filter . trelli_abundance_boxplot . trelli_abundance_heatmap . trelli_abundance_histogram . trelli_foldchange_bar . trelli_foldchange_boxplot . trelli_foldchange_heatmap . trelli_foldchange_volcano . trelli_missingness_bar . trelli_panel_by . trelli_precheck . trelli_pvalue_filter . vector_replace . voom_wrapper . zrollup . zscore_transform . 
Some associated R codes: MSnSet2pepData.R . RcppExports.R . applyFilt.R . as.multiData.R . as.omicsData.R . as.trelliData.R . bpquant.R . combine_lipidData.R . combine_techreps.R . cor_result.R . custom_sampnames.R . dim_reduction.R . dopar.R . edata_replace.R . edata_summary.R . edata_transform.R . filter_objects.R . filter_summary.R . get_comparisons.R . group_designation.R . helper_fn.R . imd_anova.R . missingval_result.R . nonmissing_per_group.R . normRes_tests.R . norm_funcs.R . normalize_global.R . normalize_isobaric.R . normalize_loess.R . normalize_nmr.R . normalize_quantile.R . pipe.R . plot_fns.R . pmartR.R . pre_imdanova_melt.R . print_data_objects.R . print_filter_objects.R . protein_quant.R . report_dataRes.R . results_summary.R . rmd_conversion.R . seqData_wrappers.R . spans.R . statRes_class.R . subset_funcs.R . summary_isobaricnormRes.R . summary_nmrnormRes.R . summary_pmartR.R . summary_trelliData.R . surv_designation.R . survival.R . trelliPlots.R .  Full pmartR package functions and examples
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