Package: gcrma 2.77.0

Z. Wu

gcrma: Background Adjustment Using Sequence Information

Background adjustment using sequence information

Authors:Jean Wu, Rafael Irizarry with contributions from James MacDonald <[email protected]> Jeff Gentry

gcrma_2.77.0.tar.gz
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gcrma.pdf |gcrma.html✨
gcrma/json (API)
NEWS

# Install 'gcrma' in R:
install.packages('gcrma', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:gcrma-2.77.0(bioc 3.20)gcrma-2.76.0(bioc 3.19)

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

bioconductor-package

31 exports 6.44 score 23 dependencies 12 dependents 186 mentions

Last updated 2 months agofrom:be4744c700

Exports:average.for.PAVbase.profilesbase.profiles.mmbase.profiles.ncbg.adjust.affinitiesbg.adjust.constantbg.adjust.fullmodelbg.adjust.gcrmabg.adjust.mmbg.adjust.opticalbg.parameters.nscheck.probescompute.affinitiescompute.affinities.localcompute.affinities2compute.affinity.coeffast.bkggcrmagcrma.bg.transformationgcrma.bg.transformation.fastgcrma.enginegcrma.engine2getCDFgetProbePackageGSB.adjjust.gcrmajustGCRMAleft.sigmamem.bkgPAVplotBaseProfiles

Dependencies:affyaffyioaskpassBiobaseBiocGenericsBiocManagerBiostringscrayoncurlGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslpreprocessCoreR6S4VectorssysUCSC.utilsXVectorzlibbioc

gcrma1.2

Rendered fromgcrma2.0.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Spline coefficients for estimation of affinity from probe sequenceaffinity.spline.coefs
Background adjustment with sequence information (internal function)bg.adjust.affinities bg.adjust.constant bg.adjust.fullmodel bg.adjust.mm bg.adjust.optical
GCRMA background adjust (internal function)bg.adjust.gcrma
Estimation of non-specific Binding Background Parametersaverage.for.PAV bg.parameters.ns left.sigma PAV
Probe Affinity computationbase.profiles base.profiles.mm base.profiles.nc check.probes compute.affinities compute.affinities.local compute.affinities2 compute.affinity.coef plotBaseProfiles
Robust Multi-Array expression measure using sequence informationgcrma gcrma.bg.transformation gcrma.bg.transformation.fast GSB.adj
GCRMA background adjust engine(internal function)gcrma.engine
GCRMA background adjust engine(internal function)gcrma.engine2
Compute GCRMA Directly from CEL Filesjust.gcrma justGCRMA