Package: SIMAT 1.45.0

M. R. Nezami Ranjbar

SIMAT: GC-SIM-MS data processing and alaysis tool

This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user.

Authors:M. R. Nezami Ranjbar <[email protected]>

SIMAT_1.45.0.tar.gz
SIMAT_1.45.0.zip(r-4.7)SIMAT_1.45.0.zip(r-4.6)SIMAT_1.45.0.zip(r-4.5)
SIMAT_1.45.0.tgz(r-4.6-any)SIMAT_1.45.0.tgz(r-4.5-any)
SIMAT_1.45.0.tar.gz(r-4.7-any)SIMAT_1.45.0.tar.gz(r-4.6-any)
SIMAT_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SIMAT/json (API)

# Install 'SIMAT' in R:

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

Datasets:

Library - Extracted compound information from an MSL library.
RItable - Extracted RI standard information from a 'csv' file.
Run - Extracted peaks from one SIM run.
target.table - Extracted target information from a 'csv' file.
Targets - Targets information in a list.

On BioConductor:SIMAT-1.45.0(bioc 3.24)SIMAT-1.44.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology software metabolomics massspectrometry

4.26 score 4 scripts 9 mentions 16 exports 33 dependencies

Last updated from:eec66a6a75. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	148
linux-devel-x86_64	OK	166
source / vignettes	OK	198
linux-release-x86_64	OK	173
macos-release-arm64	OK	99
macos-oldrel-arm64	OK	112
windows-devel	OK	104
windows-release	OK	109
windows-oldrel	OK	127
wasm-release	OK	105

Exports:getEIC getPeak getPeakScore getRI getRIStandard getScore getTarget getTargetTable optFrag plotEIC plotTIC putTargetTable readCDF readMSL writeMSL writeResult

Dependencies:Biobase BiocGenerics biocmake cli cpp11 dir.expiry farver filelock generics ggplot2 glue gtable isoband labeling lifecycle magrittr mzR ncdf4 plyr ProtGenerics R6 RColorBrewer Rcpp reshape2 Rhdf5lib rlang S7 scales stringi stringr vctrs viridisLite withr

SIMAT Usage

Rendered fromSIMAT-vignette.Rnwusingutils::Sweave

Last update: 2018-08-03
Started: 2015-03-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
This package is for processing GC-SIM-MS data	SIMAT-package SIMAT
Get the EIC of a peak	getEIC
Get all peaks corresponding to targets in several runs	getPeak
Calculate the similarity score for all peaks	getPeakScore
Generate a calibration function	getRI
Get the RI standard information	getRIStandard
Calculate similarity score for a peak	getScore
Get target information	getTarget
Get target table information	getTargetTable
Extracted compound information from an MSL library.	Library
Fragment selection through optimization	optFrag
Plotting EIC of one peak	plotEIC
Plotting TIC of one run	plotTIC
Put target table information	putTargetTable
Read raw mass spectrometry data in netCDF files	readCDF
Read mass spectral library (MSL) files	readMSL
Extracted RI standard information from a 'csv' file.	RItable
Extracted peaks from one SIM run.	Run
Extracted target information from a 'csv' file.	target.table
Targets information in a list.	Targets
Write targets information into a file with mass spectral library (MSL) format.	writeMSL
Write analysis results to file.	writeResult