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metdna's Introduction

Overview of MetDNA

Created in 2018 by Xiaotao Shen, Xin Xiong and Ruohong Wang from Dr. Zheng-Jiang Zhu lab, Chinese Academy of Sciences.

Metabolite identification is the long-standing challenge for liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we developed MetDNA (Metabolite identification and Dysregulated Network Analysis) for the large-scale and ambiguous identification of metabolites from LC-MS/MS data sets. Users can simply import MS1 peak table, MS/MS data and sample information to perform metabolite identification and dysregulated metabolic pathway analysis. MetDNA implements a metabolic reaction network (MRN) based recursive algorithm for metabolite identification, which supports data from different LC systems (e.g., HILIC and reverse phase) and MS platforms (e.g., Agilent QTOF, Sciex TripleTOF, Thermo Orbitrap, and others).

Please click Analysis tab in MetDNA web server to start your MetDNA journey!

License

Creative Commons License This work is licensed under the Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)

metdna's People

Contributors

zhumslab avatar omicspie avatar

Stargazers

Yoshitaka Inoue avatar  avatar  avatar  avatar Jie Zhu avatar  avatar  avatar Helge Hecht avatar Hansheng XUE avatar  avatar  avatar chenziru avatar Xia Shen avatar Han Hu avatar Fujian Zheng avatar

Watchers

Jiajing-xiao avatar Dong avatar Nick Jensen avatar

metdna's Issues

Issues with installation

I have run into an error while trying to install the source code from GitHub. Here are the steps I take:
library(devtools)' 'github_install('ZhuMSLab/MetDNA

The install fails with this error message:
Error: package or namespace load failed for 'MetDNA' in namespaceExport(ns, exports): undefined exports: MetDNA

Any thoughts?

Here's my sessionInfo()
`R version 3.6.1 (2019-07-05)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] devtools_2.1.0 usethis_1.5.1

loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 rstudioapi_0.10 magrittr_1.5 pkgload_1.0.2 R6_2.4.0
[6] rlang_0.4.0 tools_3.6.1 pkgbuild_1.0.5 sessioninfo_1.1.1 cli_1.1.0
[11] withr_2.1.2 remotes_2.1.0 assertthat_0.2.1 digest_0.6.20 rprojroot_1.3-2
[16] crayon_1.3.4 processx_3.4.1 callr_3.3.1 fs_1.3.1 ps_1.3.0
[21] curl_4.0 testthat_2.2.1 memoise_1.1.0 glue_1.3.1 compiler_3.6.1
[26] desc_1.2.0 backports_1.1.4 prettyunits_1.0.2`

Request instruction manual

I had read the paper of the software, i think it's so useful for me. But the web-version is so many limitation, so i want to use the code version, Can you provide a instruction manual for the code version, to instroduce how to install and configuration the code in a linux system. Thanks so much!

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