HTDA: HTDA (High Throughput Data Analysis)

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A generic platform for High throghput data analysis.

Author
Reema Singh,Andrew M. Lynn and Yogendra Bhaskar
Date of publication
2014-06-13 20:28:30
Maintainer
Who to complain to <reemasingh.jnu@gmail.com>
License
GPL
Version
1.0

View on R-Forge

Man pages

annotate
Function for Gene-Set Enrichment Analysis
AverageScan
function to extract average mass/charge and intensity value...
DenovoAsmAnnoT
Function for denovo Transcriptomics Assembly
diffExp
Function for Differential Expression
diffExpR
Function for RNASeq Differential Expression
extract
Helper function for parse-shimadzu
FinalTable
Helper function for parse-shimadzu
gcProcess
Function for GCMS data preprocessing
HTDA-package
HTDA-High Throghput Data Analysis
IndiMsScan
Function to extract m/z and intensity from each scan of Mass...
MultiVariAnalysis
Function for Multivariant Analysis
NcmsProcessData-class
Class '"NcmsProcessData"'
Parse
Another helper function for parse-Shimadzu
parse.shimadzu
Function for parsing Shimadzy pre-processed .txt file
parse.Shimadzu-class
Class '"parse.Shimadzu"'
plotAllMsSpectra
function for plotting all Mass Spectrum
PlotChrom
Plotting gas chromatogram
plotMsSpectrum
plot individual mass spectrum
preprocess
Function for processing raw LCMS data
PreProcessData-class
Class '"PreProcessData"'
QualityDenovo
Function to check the quality of the assembled Transcriptome
rmBaseline
Baseline Correction
rnaseqProcess
Constructor for class PreProcessData
SeqAna
Function for the annotation of assembled Transcriptome
SequnecAnalysisData-class
Class '"SequnecAnalysisData"'
show-methods
~~ Methods for Function 'show' ~~

Files in this package

HTDA/DESCRIPTION
HTDA/NAMESPACE
HTDA/R
HTDA/R/AverageScan.R
HTDA/R/DeSeqAnnot.R
HTDA/R/DenovoAss.R
HTDA/R/FinalTable.R
HTDA/R/IndiMsScan.R
HTDA/R/MultiVariAnalysis.R
HTDA/R/NcmsPreProcess.R
HTDA/R/Parse.R
HTDA/R/PlotAllMsSpectra.R
HTDA/R/PlotChrom.R
HTDA/R/QualityDenovo.R
HTDA/R/RNAseq.R
HTDA/R/annotate.R
HTDA/R/diffExp.R
HTDA/R/diffExpR.R
HTDA/R/extract.R
HTDA/R/parse.shimadzu.R
HTDA/R/plotMsSpectrum.R
HTDA/R/rmBaseline.R
HTDA/inst
HTDA/inst/extdata
HTDA/inst/extdata/1.txt
HTDA/inst/extdata/DATA
HTDA/inst/extdata/DATA/Control
HTDA/inst/extdata/DATA/Control/1.cdf
HTDA/inst/extdata/DATA/Control/2.cdf
HTDA/inst/extdata/DATA/Control/3.cdf
HTDA/inst/extdata/DATA/Treated
HTDA/inst/extdata/DATA/Treated/4.cdf
HTDA/inst/extdata/DATA/Treated/5.cdf
HTDA/inst/extdata/DATA/Treated/6.cdf
HTDA/inst/extdata/DATA/Treated/7.cdf
HTDA/inst/extdata/Test
HTDA/inst/extdata/Test/122402imac40-s-c-192combined_i11.csv
HTDA/inst/extdata/Test/122402imac40-s-c-192combined_i12.csv
HTDA/inst/extdata/Test/122402imac40-s-c-192combined_i13.csv
HTDA/inst/extdata/Test/122402imac40-s-c-192combined_i14.csv
HTDA/inst/extdata/pData
HTDA/inst/extdata/pData1
HTDA/man
HTDA/man/AverageScan.Rd
HTDA/man/DenovoAsmAnnoT.Rd
HTDA/man/FinalTable.Rd
HTDA/man/HTDA-package.Rd
HTDA/man/IndiMsScan.Rd
HTDA/man/MultiVariAnalysis.Rd
HTDA/man/NcmsProcessData-class.Rd
HTDA/man/Parse.Rd
HTDA/man/PlotChrom.Rd
HTDA/man/PreProcessData-class.Rd
HTDA/man/QualityDenovo.Rd
HTDA/man/SeqAna.Rd
HTDA/man/SequnecAnalysisData-class.Rd
HTDA/man/annotate.Rd
HTDA/man/diffExp.Rd
HTDA/man/diffExpR.Rd
HTDA/man/extract.Rd
HTDA/man/gcProcess.Rd
HTDA/man/parse.Shimadzu-class.Rd
HTDA/man/parse.shimadzu.Rd
HTDA/man/plotAllMsSpectra.Rd
HTDA/man/plotMsSpectrum.Rd
HTDA/man/preprocess.Rd
HTDA/man/rmBaseline.Rd
HTDA/man/rnaseqProcess.Rd
HTDA/man/show-methods.Rd