Package: MetID 1.25.0

Zhenzhi Li

MetID: Network-based prioritization of putative metabolite IDs

This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by LC-MS.

Authors:Zhenzhi Li <[email protected]>

MetID_1.25.0.tar.gz
MetID_1.25.0.zip(r-4.5)MetID_1.25.0.zip(r-4.4)MetID_1.25.0.zip(r-4.3)
MetID_1.25.0.tgz(r-4.4-any)MetID_1.25.0.tgz(r-4.3-any)
MetID_1.25.0.tar.gz(r-4.5-noble)MetID_1.25.0.tar.gz(r-4.4-noble)
MetID_1.25.0.tgz(r-4.4-emscripten)MetID_1.25.0.tgz(r-4.3-emscripten)
MetID.pdf |MetID.html✨
MetID/json (API)

# Install 'MetID' in R:

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

Bug tracker:https://github.com/ressomlab/metid/issues

Datasets:

InchiKey - Inchikey database.
demo1 - Example of input dataset, in which colnames does not meet requirement.
demo2 - Example of input dataset, in which colnames does not meet requirement.
kegg_network - Pairs of kegg network.

On BioConductor:MetID-1.23.0(bioc 3.20)MetID-1.22.0(bioc 3.19)

assaydomain biologicalquestion infrastructure researchfield statisticalmethod technology workflowstep network kegg

5.54 score 1 stars 70 scripts 150 downloads 5 mentions 1 exports 124 dependencies

Last updated 23 days agofrom:0715d000f1. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	OK	Oct 30 2024
R-4.5-linux	OK	Oct 30 2024
R-4.4-win	NOTE	Oct 30 2024
R-4.4-mac	NOTE	Oct 30 2024
R-4.3-win	NOTE	Oct 30 2024
R-4.3-mac	NOTE	Oct 30 2024

Exports:get_scores_for_LC_MS

Dependencies:askpass base64enc BH BiocGenerics bitops brew brio bslib cachem callr ChemmineR cli clipr colorspace commonmark cpp11 crayon credentials crosstalk curl DBI desc devtools diffobj digest downlit DT ellipsis evaluate fansi farver fastmap fontawesome fs gert ggplot2 gh gitcreds glue gridExtra gtable highr htmltools htmlwidgets httpuv httr2 igraph ini isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime miniUI munsell nlme openssl pillar pkgbuild pkgconfig pkgdown pkgload png praise prettyunits processx profvis promises ps purrr R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp RCurl rematch2 remotes rjson rlang rmarkdown roxygen2 rprojroot rstudioapi rsvg rversions sass scales sessioninfo shiny sourcetools stringi stringr sys systemfonts testthat textshaping tibble tinytex urlchecker usethis utf8 vctrs viridisLite waldo whisker withr xfun xml2 xopen xtable yaml zip

Introduction to MetID

Xuchen Wang

Rendered fromIntroduction_to_MetID.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2018-07-17
Started: 2018-07-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Example of input dataset, in which colnames does not meet requirement.	demo1
Example of input dataset, in which colnames does not meet requirement.	demo2
Preprocess input file.	get_cleaned
Build network between identifications based on kegg network database.	get_kegg_network
Get scores for metabolite putative IDs by LC-MS .	get_scores_for_LC_MS
Build network between identifications based on tanimoto score.	get_tani_network
Inchikey database.	InchiKey
Pairs of kegg network.	kegg_network
MetID: A package for Network-based prioritization of putative metabolite IDs.	MetID-package MetID