Other packages > Find by keyword >

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 26 Oct. 2026.
Previous versions and publish date:
(2026-07-09 06:42), 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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

MARSS  
Multivariate Autoregressive State-Space Modeling
The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstraine ...
Download / Learn more Package Citations See dependency  
LSDsensitivity  
Sensitivity Analysis Tools for 'LSD' Simulations
Tools for sensitivity analysis of LSD simulation models. Reads object-oriented data produced by LSD ...
Download / Learn more Package Citations See dependency  
rts2  
Log-Gaussian Cox Process Models with Approximations
Supports modelling real-time case data to facilitate the real-time surveillance of infectious disea ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
SADEG  
Stability Analysis in Differentially Expressed Genes
We analyzed the nucleotide composition of genes with a special emphasis on stability of DNA sequence ...
Download / Learn more Package Citations See dependency  

29,218

R Packages

247,686

Dependencies

77,281

Author Associations

29,219

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA