Introduction | What's new in version 2.0.0 | Options for gcrma | Getting started: the simplest example | More Examples with options | Efficient use of gcrma
Package: gcrma 2.85.0
Z. Wu
gcrma: Background Adjustment Using Sequence Information
Background adjustment using sequence information
Authors:
gcrma_2.85.0.tar.gz
gcrma_2.85.0.zip(r-4.7)gcrma_2.85.0.zip(r-4.6)gcrma_2.85.0.zip(r-4.5)
gcrma_2.85.0.tgz(r-4.6-x86_64)gcrma_2.85.0.tgz(r-4.6-arm64)gcrma_2.85.0.tgz(r-4.5-x86_64)gcrma_2.85.0.tgz(r-4.5-arm64)
gcrma_2.85.0.tar.gz(r-4.7-arm64)gcrma_2.85.0.tar.gz(r-4.7-x86_64)gcrma_2.85.0.tar.gz(r-4.6-arm64)gcrma_2.85.0.tar.gz(r-4.6-x86_64)
gcrma_2.85.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gcrma/json (API)
| # Install 'gcrma' in R: |
| install.packages('gcrma', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- affinity.spline.coefs - Spline coefficients for estimation of affinity from probe sequence
On BioConductor:gcrma-2.85.0(bioc 3.24)gcrma-2.84.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarrayonechannelpreprocessing
Last updated from:b5a7b90c54. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 227 | ||
| linux-devel-arm64 | NOTE | 211 | ||
| linux-devel-x86_64 | NOTE | 274 | ||
| source / vignettes | OK | 244 | ||
| linux-release-arm64 | NOTE | 191 | ||
| linux-release-x86_64 | NOTE | 259 | ||
| macos-release-arm64 | NOTE | 167 | ||
| macos-release-x86_64 | NOTE | 259 | ||
| macos-oldrel-arm64 | NOTE | 237 | ||
| macos-oldrel-x86_64 | NOTE | 251 | ||
| windows-devel | NOTE | 502 | ||
| windows-release | NOTE | 475 | ||
| windows-oldrel | NOTE | 512 | ||
| wasm-release | OK | 238 |
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:affyaffyioBiobaseBiocGenericsBiocManagerBiostringscrayongenericsIRangespreprocessCoreS4VectorsSeqinfoXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Spline coefficients for estimation of affinity from probe sequence | affinity.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 Parameters | average.for.PAV bg.parameters.ns left.sigma PAV |
| Probe Affinity computation | base.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 information | gcrma 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 Files | just.gcrma justGCRMA |