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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SIMAT")
AuthorMo R. Nezami Ranjbar <nranjbar@vt.edu>
Bioconductor views MassSpectrometry Metabolomics Software
Date of publicationNone
MaintainerMo R. Nezami Ranjbar <nranjbar@vt.edu>
LicenseGPL-2
Version1.6.1
http://omics.georgetown.edu/SIMAT.html

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/getEIC.R R/getPeak.R R/getPeakScore.R R/getRI.R R/getRIStandard.R R/getScore.R R/getTarget.R R/getTargetTable.R R/optFrag.R R/plotEIC.R R/plotTIC.R R/putTargetTable.R R/readCDF.R R/readMSL.R R/writeMSL.R
SIMAT
build
build/vignette.rds
data
data/Library.rda
data/RItable.rda
data/Run.rda
data/Targets.rda
data/target.table.rda
inst
inst/doc
inst/doc/SIMAT-vignette.R
inst/doc/SIMAT-vignette.Rnw
inst/doc/SIMAT-vignette.pdf
inst/extdata
inst/extdata/1_QC.CDF
inst/extdata/RIStandards.csv
inst/extdata/TargetTable.txt
inst/extdata/Targets_1.MSL
inst/unitTests
inst/unitTests/test_getEIC.R inst/unitTests/test_getPeak.R inst/unitTests/test_getPeakScore.R inst/unitTests/test_getRI.R inst/unitTests/test_getRIStandard.R inst/unitTests/test_getScore.R inst/unitTests/test_getTarget.R inst/unitTests/test_getTargetTable.R inst/unitTests/test_optFrag.R inst/unitTests/test_plotEIC.R inst/unitTests/test_plotTIC.R inst/unitTests/test_putTargetTable.R inst/unitTests/test_readCDF.R inst/unitTests/test_readMSL.R inst/unitTests/test_writeMSL.R
man
man/Library.Rd man/RItable.Rd man/Run.Rd man/SIMAT-package.Rd man/Targets.Rd man/getEIC.Rd man/getPeak.Rd man/getPeakScore.Rd man/getRI.Rd man/getRIStandard.Rd man/getScore.Rd man/getTarget.Rd man/getTargetTable.Rd man/optFrag.Rd man/plotEIC.Rd man/plotTIC.Rd man/putTargetTable.Rd man/readCDF.Rd man/readMSL.Rd man/target.table.Rd man/writeMSL.Rd
tests
tests/runTests.R
vignettes
vignettes/SIMAT-vignette.Rnw
vignettes/dsPeaks.rds

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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