Package: MsBackendMongoDb 0.97.3

Johannes Rainer

MsBackendMongoDb: NoSQL-based Mass Spectrometry Data Backend

Mass spectrometry (MS) data backend for data storage in NoSQL MongoDB dagabases. Objects from this package expand the data storage and handling infrastructure of the Spectra Bioconductor package. This package adds support to store and retrieve MS data from MongoDB databases.

Authors:Ahlam Mentag [aut], Johannes Rainer [aut, cre]

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manual.pdf |manual.html✨
card.svg |card.png
MsBackendMongoDb/json (API)

# Install 'MsBackendMongoDb' in R:

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

Bug tracker:https://github.com/rformassspectrometry/msbackendmongodb/issues

On CRAN:

infrastructure massspectrometry metabolomics dataimport proteomics

2.18 score 17 exports 31 dependencies

Last updated from:8666897aa2. Checks:8 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	195
source / vignettes	ERROR	220
linux-release-x86_64	ERROR	189
macos-release-arm64	ERROR	143
macos-oldrel-arm64	ERROR	171
windows-devel	ERROR	159
windows-release	ERROR	151
windows-oldrel	ERROR	169
wasm-release	OK	143

Exports:backendInitialize connectMsBackendMongoDb dataStorage extractByIndex intensity intensity<-MsBackendMongoDb mz mz<-peaksData peaksVariables reset show spectraData spectraNames spectraNames<-supportsSetBackend

Dependencies:askpass BH BiocGenerics BiocParallel clue cluster codetools cpp11 data.table DBI fastmatch formatR fs futile.logger futile.options generics IRanges jsonlite lambda.r MASS MetaboCoreUtils mime mongolite MsCoreUtils openssl ProtGenerics Rcpp S4Vectors snow Spectra sys

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create a connection to MongoDb	connectMsBackendMongoDb
'Spectra' MS backend storing data in a MongoDb database	backendInitialize,MsBackendMongoDb-method dataStorage,MsBackendMongoDb-method extractByIndex,MsBackendMongoDb,ANY-method extractByIndex,MsBackendMongoDb-method intensity,MsBackendMongoDb-method intensity<-,MsBackendMongoDb-method MsBackendMongoDb MsBackendMongoDb-class mz,MsBackendMongoDb-method mz<-,MsBackendMongoDb-method peaksData,MsBackendMongoDb-method peaksVariables,MsBackendMongoDb-method reset,MsBackendMongoDb-method show,MsBackendMongoDb-method spectraData,MsBackendMongoDb-method spectraNames,MsBackendMongoDb-method spectraNames<-,MsBackendMongoDb-method supportsSetBackend,MsBackendMongoDb-method [,MsBackendMongoDb-method

Help page

Topics

Create a connection to MongoDb

connectMsBackendMongoDb

'Spectra' MS backend storing data in a MongoDb database

backendInitialize,MsBackendMongoDb-method dataStorage,MsBackendMongoDb-method extractByIndex,MsBackendMongoDb,ANY-method extractByIndex,MsBackendMongoDb-method intensity,MsBackendMongoDb-method intensity<-,MsBackendMongoDb-method MsBackendMongoDb MsBackendMongoDb-class mz,MsBackendMongoDb-method mz<-,MsBackendMongoDb-method peaksData,MsBackendMongoDb-method peaksVariables,MsBackendMongoDb-method reset,MsBackendMongoDb-method show,MsBackendMongoDb-method spectraData,MsBackendMongoDb-method spectraNames,MsBackendMongoDb-method spectraNames<-,MsBackendMongoDb-method supportsSetBackend,MsBackendMongoDb-method [,MsBackendMongoDb-method