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| bcbioBase-package | bcbioBase |
| as | Methods for Coercing an Object to a Class |
| assertFormalAnnotationCol | Assert Formal Annotation Column |
| assertFormalInterestingGroups | Interesting Groups Formal Assert Check |
| bcbioBase | bcbioBase |
| coerce | Methods for Coercing an Object to a Class |
| coerce-SummarizedExperiment-list | Methods for Coercing an Object to a Class |
| convertGenesToSymbols | Convert Genes to Symbols |
| convertGenesToSymbols-method | Convert Genes to Symbols |
| copyToDropbox | Copy Files to Dropbox |
| counts | Counts |
| counts-method | Counts |
| flatFiles | Flat Files from S4 Object |
| flatFiles-method | Flat Files from S4 Object |
| gene2symbol | Gene to Symbol Mappings |
| gene2symbol-method | Gene to Symbol Mappings |
| interestingGroups | Interesting Groups |
| interestingGroups-method | Interesting Groups |
| interestingGroups<- | Interesting Groups |
| interestingGroups<--method | Interesting Groups |
| plotCorrelationHeatmap | Plot Correlation Heatmap |
| plotCorrelationHeatmap-method | Plot Correlation Heatmap |
| plotHeatmap | Plot Heatmap |
| plotHeatmap-method | Plot Heatmap |
| plotQuantileHeatmap | Plot Heatmap with Quantile Breaks |
| plotQuantileHeatmap-method | Plot Heatmap with Quantile Breaks |
| prepareSummarizedExperiment | Prepare Summarized Experiment |
| prepareTemplate | Prepare R Markdown Template File |
| readDataVersions | Read Data Versions |
| readLog | Read Log File |
| readProgramVersions | Read Program Versions |
| readSampleData | Read Sample Metadata |
| readTx2gene | Transcript to Gene Annotations |
| readYAML | Read YAML Sample Data and Metrics |
| readYAMLSampleData | Read YAML Sample Data and Metrics |
| readYAMLSampleMetrics | Read YAML Sample Data and Metrics |
| rse_bcb | 'RangedSummarizedExperiment' Coerced from 'bcbioRNASeq' |
| rse_dds | 'RangedSummarizedExperiment' Coerced from 'DESeqDataSet' |
| sampleData | Sample Data |
| sampleData-method | Sample Data |
| sampleData<- | Sample Data |
| sampleData<--method | Sample Data |
| sampleDirs | Sample Directories |
| selectSamples | Select Samples |
| selectSamples-method | Select Samples |
| uniteInterestingGroups | Unite Interesting Groups |
| uniteInterestingGroups-method | Unite Interesting Groups |