Package: notameStats 1.3.0

Vilhelm Suksi

notameStats: Workflow for non-targeted LC-MS metabolic profiling

Provides univariate and multivariate statistics for feature prioritization in untargeted LC-MS metabolomics research.

Authors:Anton Klåvus [aut, cph], Jussi Paananen [aut, cph], Oskari Timonen [aut, cph], Atte Lihtamo [aut], Vilhelm Suksi [aut, cre], Retu Haikonen [aut], Leo Lahti [aut], Kati Hanhineva [aut], Ville Koistinen [ctb], Olli Kärkkäinen [ctb], Artur Sannikov [ctb]

notameStats_1.3.0.tar.gz
notameStats_1.3.0.zip(r-4.7)notameStats_1.3.0.zip(r-4.6)notameStats_1.3.0.zip(r-4.5)
notameStats_1.3.0.tgz(r-4.6-any)notameStats_1.3.0.tgz(r-4.5-any)
notameStats_1.3.0.tar.gz(r-4.7-any)notameStats_1.3.0.tar.gz(r-4.6-any)
notameStats_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
notameStats/json (API)

# Install 'notameStats' in R:

install.packages('notameStats', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hanhineva-lab/notamestats/issues

On BioConductor:notameStats-1.3.0(bioc 3.24)notameStats-1.2.0(bioc 3.23)

biomedicalinformatics metabolomics dataimport massspectrometry batcheffect multiplecomparison normalization qualitycontrol visualization preprocessing

4.95 score 5 scripts 206 downloads 25 exports 59 dependencies

Last updated from:66400ee40b. Checks:6 NOTE, 2 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	209
linux-devel-x86_64	ERROR	440
source / vignettes	OK	346
linux-release-x86_64	NOTE	432
macos-release-arm64	NOTE	232
macos-oldrel-arm64	NOTE	323
windows-devel	ERROR	1767
windows-release	NOTE	1753
windows-oldrel	NOTE	1665
wasm-release	OK	171

Exports:cohens_d fit_rf fold_change importance_rf mixomics_pls mixomics_pls_optimize mixomics_plsda mixomics_plsda_optimize mixomics_spls_optimize mixomics_splsda_optimize muvr_analysis perform_auc perform_correlation_tests perform_homoscedasticity_tests perform_kruskal_wallis perform_lm perform_lm_anova perform_lmer perform_logistic perform_non_parametric perform_oneway_anova perform_permanova perform_t_test summarize_results summary_statistics

Dependencies:abind backports BH Biobase BiocGenerics BiocParallel broom cli codetools cpp11 DelayedArray dplyr farver formatR futile.logger futile.options generics GenomicRanges ggplot2 glue gtable IRanges isoband labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats notame openxlsx pillar pkgconfig purrr R6 RColorBrewer Rcpp rlang S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector zip

Non-targeted metabolomics feature prioritization

Rendered fromNon-targeted_metabolomics_feature_prioritization.Rmdusingknitr::rmarkdown

Last update: 2025-09-08
Started: 2025-09-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cohen's D	cohens_d
Fit Random Forest	fit_rf
Fold change	fold_change
Feature importance in random forest	importance_rf
Multivariate modelling with minimally biased variable selection (MUVR)	muvr_analysis
Area under curve	perform_auc
Correlation test	perform_correlation_tests
Test homoscedasticity	perform_homoscedasticity_tests
Kruskal-Wallis rank-sum test	perform_kruskal_wallis
Linear models	perform_lm
Linear models ANOVA table	perform_lm_anova
Linear mixed models	perform_lmer
Logistic regression	perform_logistic
Pairwise and paired non-parametric tests	perform_non_parametric
Welch's ANOVA and classic ANOVA	perform_oneway_anova
PERMANOVA	perform_permanova
Pairwise and paired t-tests	perform_t_test
PLS	mixomics_pls mixomics_pls_optimize mixomics_spls_optimize pls
PLS-DA	mixomics_plsda mixomics_plsda_optimize mixomics_splsda_optimize pls_da
Statistics cleaning	summarize_results
Summary statistics	summary_statistics