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.Rbuildignore (547, 2023-09-02)
DESCRIPTION (1256, 2023-09-02)
LICENSE (1065, 2023-09-02)
NAMESPACE (4657, 2023-09-02)
NEWS.md (828, 2023-09-02)
R/ (0, 2023-09-02)
R/10_MASSBANK.R (16781, 2023-09-02)
R/11_MONA.R (8872, 2023-09-02)
R/12_NIST.R (12012, 2023-09-02)
R/13_LIPIDMAPS.R (10581, 2023-09-02)
R/14_FOODB.R (23330, 2023-09-02)
R/15_PUBCHEM.R (8242, 2023-09-02)
R/15_WIKIPEDIA.R (5018, 2023-09-02)
R/16_KEGG.R (21808, 2023-09-02)
R/16_KEGG_pathway.R (7389, 2023-09-02)
R/17_RHEA.R (16286, 2023-09-02)
R/18_METACYC.R (1872, 2023-09-02)
R/19_REACTOME.R (2611, 2023-09-02)
R/1_massdatabase_logo.R (2293, 2023-09-02)
R/2_global_variables.R (3401, 2023-09-02)
R/3_utils.R (14545, 2023-09-02)
R/4_data.R (414, 2023-09-02)
R/5_BIGG.R (31991, 2023-09-02)
R/6_CHEBI.R (24228, 2023-09-02)
R/7_GNPS.R (11209, 2023-09-02)
R/8_HMDB.R (17147, 2023-09-02)
R/8_SMPDB_PATHWAY.R (8464, 2023-09-02)
R/9_LIPIDBANK.R (19883, 2023-09-02)
R/attach.R (1699, 2023-09-02)
R/convert2metid.R (9096, 2023-09-02)
R/get_words_similarity.R (1416, 2023-09-02)
R/read_msp_data.R (23328, 2023-09-02)
R/read_pwml.R (0, 2023-09-02)
R/read_sbml_data.R (12091, 2023-09-02)
R/read_xml_data.R (10611, 2023-09-02)
R/utils.R (1364, 2023-09-02)
R/zzz.R (484, 2023-09-02)
_pkgdown.yml (5385, 2023-09-02)
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# massDatabase [](https://cran.r-project.org/package=massdatabase) [](https://github.com/tidymass/massdatabase) [](https://cran.r-project.org/package=massdatabase) [](https://www.tidyverse.org/lifecycle/#experimental) `massdatabase` is a part of [tidymass](https://tidymass.github.io/tidymass/) ------- # About `massdatabase` is an R package that operates the online public databases and combines with other tools for streamlined compound annotation and pathway enrichment analysis. `massDatabase` is a flexible, simple, and powerful tool that can be installed on all platforms, allowing the users to leverage all the online public databases for biological function mining. # Installation You can install `massdatabase` from [GitLab](https://gitlab.com/jaspershen/massdatabase) ``` r if(!require(remotes)){ install.packages("remotes") } remotes::install_gitlab("jaspershen/massdatabase") ``` or [Github](https://github.com/tidymass/massdatabase) ``` r remotes::install_github("tidymass/massdatabase") ``` # Usage Please see the `Help documents` page to get the instruction of `massDatabase`. ## Need help? If you have any questions about `massdatabase`, please don’t hesitate to email me (). [shenzutao1990](https://www.shenxt.info/files/wechat_QR.jpg) [Twitter](https://twitter.com/xiaotaoshen1990) [M339, Alway Buidling, Cooper Lane, Palo Alto, CA 94304](https://www.google.com/maps/place/Alway+Building/@37.4322345,-122.1770883,17z/data=!3m1!4b1!4m5!3m4!1s0x808fa4d335c3be37:0x9057931f3b312c29!8m2!3d37.4322345!4d-122.1748996) # Citation If you use `massdatabase` in your publications, please cite this paper: 1. massDatabase: utilities for the operation of the public compound and pathway database. [Web Link](https://www.biorxiv.org/content/10.1101/2022.06.02.494457v1) 2. Shen, X., Yan, H., Wang, C. et al. TidyMass an object-oriented reproducible analysis framework for LC–MS data. Nat Commun 13, 4365 (2022). [Web Link](https://www.nature.com/articles/s41467-022-32155-w). Thanks very much!

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