Package: MetAlyzer 1.0.0

MetAlyzer: Read and Analyze 'MetIDQ™' Software Output Files

The 'MetAlyzer' S4 object provides methods to read and reformat metabolomics data for convenient data handling, statistics and downstream analysis. The resulting format corresponds to input data of the Shiny app 'MetaboExtract' (<https://www.metaboextract.shiny.dkfz.de/MetaboExtract/>).

Authors:Nils Mechtel [aut, cre], Luis Herfurth [aut], Carolin Andresen [aut], Daniel Huebschmann [aut]

MetAlyzer_1.0.0.tar.gz
MetAlyzer_1.0.0.zip(r-4.5)MetAlyzer_1.0.0.zip(r-4.4)MetAlyzer_1.0.0.zip(r-4.3)
MetAlyzer_1.0.0.tgz(r-4.4-any)MetAlyzer_1.0.0.tgz(r-4.3-any)
MetAlyzer_1.0.0.tar.gz(r-4.5-noble)MetAlyzer_1.0.0.tar.gz(r-4.4-noble)
MetAlyzer_1.0.0.tgz(r-4.4-emscripten)MetAlyzer_1.0.0.tgz(r-4.3-emscripten)
MetAlyzer.pdf |MetAlyzer.html✨
MetAlyzer/json (API)
NEWS

# Install 'MetAlyzer' in R:

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

Bug tracker:https://github.com/nilsmechtel/metalyzer/issues

On CRAN:

5.61 score 3 stars 4 scripts 252 downloads 24 exports 98 dependencies

Last updated 1 months agofrom:f499669e4e. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 21 2024
R-4.5-win	OK	Nov 21 2024
R-4.5-linux	OK	Nov 21 2024
R-4.4-win	OK	Nov 21 2024
R-4.4-mac	OK	Nov 21 2024
R-4.3-win	OK	Nov 21 2024
R-4.3-mac	OK	Nov 21 2024

Exports:aggregatedData calculate_anova calculate_cv calculate_log2FC example_extraction_data example_meta_data example_mutation_data_xl exportConcValues filterMetabolites filterMetaData log2FC metalyzer_colors MetAlyzer_dataset pathway plot_log2FC plot_network plotly_network plotly_scatter plotly_vulcano polarity renameMetaData summarizeConcValues summarizeQuantData updateMetaData

Dependencies:abind agricolae AlgDesign askpass base64enc Biobase BiocGenerics bslib cachem cli cluster colorspace cpp11 crayon crosstalk curl data.table DelayedArray digest dplyr evaluate fansi farver fastmap fontawesome fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel glue gridExtra gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl openxlsx pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S4Arrays S4Vectors sass scales SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridis viridisLite withr xfun XVector yaml zip zlibbioc

MetAlyzer User Guide

Nils Mechtel, Carolin Andresen & Luis Herfurth

Rendered fromMetAlyzer_User_Guide.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-03-10
Started: 2022-01-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get Aggregated Data	aggregatedData
One-way ANOVA	calculate_anova
Add mean, SD and CV	calculate_cv
Calculate log2 fold change	calculate_log2FC
Get example extraction data	example_extraction_data
Get example meta data	example_meta_data
Get example mutation data	example_mutation_data_xl
Export filtered raw data as csv	exportConcValues
Filter metabolites	filterMetabolites
Filter meta data	filterMetaData
Get log2FC Data	log2FC
Get MetAlyzer colors	metalyzer_colors
Open file and read data	MetAlyzer_dataset
Get pathway file path	pathway
Plot log2 fold change	plot_log2FC
Plot Pathway Network	plot_network
Plotly Log2FC Network Plot	plotly_network
Plotly Log2FC Scatter Plot	plotly_scatter
Plotly Log2FC Vulcano Plot	plotly_vulcano
Get polarity file path	polarity
Read Named Regions	read_named_region
Rename meta data	renameMetaData
Summarize concentration values	summarizeConcValues
Summarize quantification status	summarizeQuantData
Update meta data	updateMetaData