Man pages for pkimes/upbm
Tools for the analysis of universal protein binding microarrays

backgroundSubtractBackground subtract intensities
cy3FitEmpiricalCompute Cy3 scaling factors using emprical reference
cy3FitModelCompute Cy3 scaling factors using regression
cy3GenerateRefGenerate Cy3 empirical reference
cy3NormalizePerform Cy3 normalization
dl2_estimatorDerSimonian and Kacker estimator
dl_estimatorDerSimonian and Laird estimator
fitProbeDistributionFit Probe-Level Convolution Distributions
gpr2PBMExperimentLoad raw PBM scan data as PBMExperiment
kmerFitFit k-mer probe set models
kmerTestAffinityTest for k-mer preferential affinities
kmerTestContrastTest for k-mer differential affinities
kmerTestSpecificityTest for k-mer differential specificities
mapKmersMap K-mer Motifs to PBM Probe Sequences
normalizeAcrossReplicatesNormalize across replicates
normalizeWithinReplicatesNormalize within replicates
PBMclass-accessorsPBM slot accessors and setters
PBMDesignCreate a new PBMDesign object
PBMDesign-classPBMDesign class
PBMDesign-replaceSet design in PBMExperiment object
PBMExperimentCreate a new PBMExperiment object
PBMExperiment-classPBMExperiment class
pbmFilterProbesFilter PBMExperiment and PBMDesign objects
pbmTrimProbesTrim probe sequences
probeFitFit probe models
readGPRRead GPR File
show-methodsShow upbm objects
spatiallyAdjustPerform spatial adjustment
summarizeKmersCompute K-mer summary metrics from probe intensities
tidy-PBMExperimentTidy PBMExperiment object
tidy-SummarizedExperimentTidy SummarizedExperiment object
uniqueKmersGenerate Unique K-mer Sequences
upbm-packageupbm
upbmPreprocessPBM Preprocess
pkimes/upbm documentation built on Nov. 8, 2019, 9:33 a.m.