Package: gcrma 2.79.0

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_2.79.0.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-2.79.0(bioc 3.21)gcrma-2.78.0(bioc 3.20)

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

microarrayonechannelpreprocessing

7.32 score 12 packages 164 scripts 1.8k downloads 186 mentions 31 exports 23 dependencies

Last updated 3 months agofrom:7375785312. Checks:1 OK, 1 ERROR, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 14 2025
R-4.5-win-x86_64NOTEJan 14 2025
R-4.5-linux-x86_64ERRORJan 14 2025
R-4.4-win-x86_64NOTEJan 14 2025
R-4.4-mac-x86_64NOTEJan 14 2025
R-4.4-mac-aarch64NOTEJan 14 2025
R-4.3-win-x86_64NOTEJan 14 2025
R-4.3-mac-x86_64NOTEJan 14 2025
R-4.3-mac-aarch64NOTEJan 14 2025

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:affyaffyioaskpassBiobaseBiocGenericsBiocManagerBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslpreprocessCoreR6S4VectorssysUCSC.utilsXVector

gcrma1.2

Rendered fromgcrma2.0.Rnwusingutils::Sweaveon Jan 14 2025.

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