Man pages for pkimes/upbm
Tools for the analysis of universal protein binding microarrays
| backgroundSubtract | Background subtract intensities |
| cy3FitEmpirical | Compute Cy3 scaling factors using emprical reference |
| cy3FitModel | Compute Cy3 scaling factors using regression |
| cy3GenerateRef | Generate Cy3 empirical reference |
| cy3Normalize | Perform Cy3 normalization |
| dl2_estimator | DerSimonian and Kacker estimator |
| dl_estimator | DerSimonian and Laird estimator |
| fitProbeDistribution | Fit Probe-Level Convolution Distributions |
| gpr2PBMExperiment | Load raw PBM scan data as PBMExperiment |
| kmerFit | Fit k-mer probe set models |
| kmerTestAffinity | Test for k-mer preferential affinities |
| kmerTestContrast | Test for k-mer differential affinities |
| kmerTestSpecificity | Test for k-mer differential specificities |
| mapKmers | Map K-mer Motifs to PBM Probe Sequences |
| normalizeAcrossReplicates | Normalize across replicates |
| normalizeWithinReplicates | Normalize within replicates |
| PBMclass-accessors | PBM slot accessors and setters |
| PBMDesign | Create a new PBMDesign object |
| PBMDesign-class | PBMDesign class |
| PBMDesign-replace | Set design in PBMExperiment object |
| PBMExperiment | Create a new PBMExperiment object |
| PBMExperiment-class | PBMExperiment class |
| pbmFilterProbes | Filter PBMExperiment and PBMDesign objects |
| pbmTrimProbes | Trim probe sequences |
| probeFit | Fit probe models |
| readGPR | Read GPR File |
| show-methods | Show upbm objects |
| spatiallyAdjust | Perform spatial adjustment |
| summarizeKmers | Compute K-mer summary metrics from probe intensities |
| tidy-PBMExperiment | Tidy PBMExperiment object |
| tidy-SummarizedExperiment | Tidy SummarizedExperiment object |
| uniqueKmers | Generate Unique K-mer Sequences |
| upbm-package | upbm |
| upbmPreprocess | PBM Preprocess |
