Package: MetID 1.30.0

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_1.30.0.tar.gz
MetID_1.30.0.zip(r-4.7-any)MetID_1.30.0.zip(r-4.6-any)MetID_1.30.0.zip(r-4.5-any)
MetID_1.30.0.tgz(r-4.6-any)MetID_1.30.0.tgz(r-4.5-any)
MetID_1.30.0.tar.gz(r-4.7-any)MetID_1.30.0.tar.gz(r-4.6-any)
MetID_1.30.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MetID/json (API)

# Install 'MetID' in R:

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

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

Datasets:

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

On BioConductor:MetID-1.31.0(bioc 3.24)MetID-1.30.0(bioc 3.23)

assaydomain biologicalquestion infrastructure researchfield statisticalmethod technology workflowstep network kegg

5.79 score 1 stars 124 scripts 375 downloads 5 mentions 1 exports 120 dependencies

Last updated from:3719192b57 (on RELEASE_3_23). Checks:4 ERROR, 6 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	197
linux-devel-x86_64	OK	250
source / vignettes	OK	265
linux-release-x86_64	ERROR	231
macos-release-arm64	ERROR	125
macos-oldrel-arm64	ERROR	129
windows-devel	OK	140
windows-release	OK	148
windows-oldrel	OK	150
wasm-release	OK	187

Exports:get_scores_for_LC_MS

Dependencies:askpass base64enc BH BiocGenerics bitops brew brio bslib cachem callr ChemmineR cli clipr commonmark cpp11 crayon credentials crosstalk curl DBI desc devtools diffobj digest downlit DT ellipsis evaluate fansi farver fastmap fontawesome fs generics gert ggplot2 gitcreds glue gridExtra gtable highr htmltools htmlwidgets httpuv httr2 igraph ini isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr Matrix memoise mime miniUI openssl otel pak pillar pkgbuild pkgconfig pkgdown pkgload png praise prettyunits processx profvis promises ps purrr R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp RCurl rjson rlang rmarkdown roxygen2 rprojroot rstudioapi rsvg rversions S7 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

Rendered fromIntroduction_to_MetID.Rmdusingknitr::rmarkdown

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