Package: gcrma 2.79.0
Z. Wu
gcrma: Background Adjustment Using Sequence Information
Background adjustment using sequence information
Authors:
gcrma_2.79.0.tar.gz
gcrma_2.79.0.zip(r-4.5)gcrma_2.79.0.zip(r-4.4)gcrma_2.79.0.zip(r-4.3)
gcrma_2.79.0.tgz(r-4.4-x86_64)gcrma_2.79.0.tgz(r-4.4-arm64)gcrma_2.79.0.tgz(r-4.3-x86_64)gcrma_2.79.0.tgz(r-4.3-arm64)
gcrma_2.79.0.tar.gz(r-4.5-noble)gcrma_2.79.0.tar.gz(r-4.4-noble)
gcrma_2.79.0.tgz(r-4.4-emscripten)gcrma_2.79.0.tgz(r-4.3-emscripten)
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')) |
- affinity.spline.coefs - Spline coefficients for estimation of affinity from probe sequence
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
Last updated 2 months agofrom:7375785312. Checks:OK: 1 ERROR: 1 NOTE: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 29 2024 |
| R-4.5-linux-x86_64 | ERROR | Nov 29 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 29 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 29 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 29 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 29 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 29 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 29 2024 |
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.utilsXVectorzlibbioc
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 |