| .calc_RLE |
Source code
|
| .calc_top_prop |
Source code
|
| .call_Salmon |
Source code
|
| .call_kallisto |
Source code
|
| .checkedCall |
Source code
|
| .choose_vis_values |
Source code
|
| .compute_ave_count |
Source code
|
| .compute_exprs |
Source code
|
| .construct_sf_field |
Source code
|
| .countToEffCounts |
Source code
|
| .countToFpkm |
Source code
|
| .countToTpm |
Source code
|
| .exprs_hunter |
Source code
|
| .fcontrol_names |
Source code
|
| .find_control_SF |
Source code
|
| .fpkmToTpm |
Source code
|
| .getRSquared |
Source code
|
| .getTypeOfVariable |
Source code
|
| .get_exprs_for_RLE |
Source code
|
| .get_palette |
Source code
|
| .get_qc_metrics_exprs_mat |
Source code
|
| .magic_default |
Source code
|
| .makePairs |
Source code
|
| .plotRLE |
Source code
|
| .plotRLE_full |
Source code
|
| .plotRLE_minimal |
Source code
|
| .process_feature_controls |
Source code
|
| .recompute_expr_fun |
Source code
|
| .resolve_plot_colours |
Source code
|
| .rle_boxplot_stats |
Source code
|
| .spike_fcontrol_names |
Source code
|
| .subset2index |
Source code
|
| SCESet |
Man page
|
| SCESet-class |
Man page
|
| SCESet-subset |
Man page
|
| [,SCESet,ANY,ANY,ANY-method |
Man page
|
| [,SCESet,ANY,ANY-method |
Man page
|
| [,SCESet,ANY-method |
Man page
|
| areSizeFactorsCentred |
Man page
Source code
|
| arrange |
Man page
Man page
|
| arrange,SCESet-method |
Man page
Man page
|
| arrange.SCESet |
Man page
Source code
|
| bootstraps |
Man page
Man page
Man page
Man page
|
| bootstraps,SCESet-method |
Man page
Man page
|
| bootstraps.SCESet |
Man page
Source code
|
| bootstraps<- |
Man page
Man page
|
| bootstraps<-,SCESet,array-method |
Man page
|
| calcAverage |
Man page
Source code
|
| calcIsExprs |
Man page
Source code
|
| calculateCPM |
Man page
Source code
|
| calculateFPKM |
Man page
Source code
|
| calculateQCMetrics |
Man page
Source code
|
| calculateTPM |
Man page
Source code
|
| cellDist |
Man page
|
| cellDist,SCESet-method |
Man page
Man page
|
| cellDist<- |
Man page
Man page
Man page
|
| cellDist<-,SCESet,dist-method |
Man page
|
| cellDist<-,SCESet,matrix-method |
Man page
|
| cellDistSCESet |
Man page
Source code
|
| cellNames |
Man page
Man page
Source code
|
| cellNames<- |
Man page
|
| cellNames<-,SCESet,vector-method |
Man page
|
| cellPairwiseDistances |
Man page
Man page
Man page
Man page
Man page
Man page
Man page
Man page
Man page
|
| cellPairwiseDistances,SCESet-method |
Man page
Man page
|
| cellPairwiseDistances.SCESet |
Man page
Source code
|
| cellPairwiseDistances<- |
Man page
Man page
Man page
|
| cellPairwiseDistances<-,SCESet,dist-method |
Man page
|
| cellPairwiseDistances<-,SCESet,matrix-method |
Man page
|
| counts |
Man page
Man page
|
| counts,SCESet-method |
Man page
Man page
|
| counts.SCESet |
Man page
Source code
|
| counts<-,SCESet,matrix-method |
Man page
|
| cpm |
Man page
Man page
Man page
|
| cpm,SCESet-method |
Man page
Man page
|
| cpm<- |
Man page
Man page
|
| cpm<-,SCESet,matrix-method |
Man page
Man page
|
| cpmSCESet |
Man page
Source code
|
| fData |
Man page
Man page
|
| fData,SCESet-method |
Man page
|
| fData<-,SCESet,AnnotatedDataFrame-method |
Man page
|
| fData<-,SCESet,data.frame-method |
Man page
|
| featDist |
Man page
Man page
|
| featDist,SCESet-method |
Man page
Man page
|
| featDist<- |
Man page
Man page
Man page
|
| featDist<-,SCESet,dist-method |
Man page
|
| featDist<-,SCESet,matrix-method |
Man page
|
| featDistSCESet |
Man page
Source code
|
| featureControlInfo |
Man page
Man page
Man page
Man page
|
| featureControlInfo,SCESet-method |
Man page
Man page
|
| featureControlInfo.SCESet |
Man page
Source code
|
| featureControlInfo<- |
Man page
Man page
Man page
|
| featureControlInfo<-,SCESet,AnnotatedDataFrame-method |
Man page
|
| featurePairwiseDistances |
Man page
Man page
Man page
Man page
Man page
Man page
Man page
Man page
Man page
|
| featurePairwiseDistances,SCESet-method |
Man page
Man page
|
| featurePairwiseDistances<- |
Man page
Man page
Man page
|
| featurePairwiseDistances<-,SCESet,dist-method |
Man page
|
| featurePairwiseDistances<-,SCESet,matrix-method |
Man page
|
| featurePairwiseDistancesSCESet |
Man page
Source code
|
| filter |
Man page
Man page
|
| filter,SCESet-method |
Man page
Man page
|
| filter.SCESet |
Man page
Source code
|
| findImportantPCs |
Man page
Source code
|
| fpkm |
Man page
Man page
Man page
|
| fpkm,SCESet-method |
Man page
Man page
|
| fpkm.SCESet |
Man page
Source code
|
| fpkm<- |
Man page
Man page
|
| fpkm<-,SCESet,matrix-method |
Man page
Man page
|
| fromCellDataSet |
Man page
Source code
|
| getBMFeatureAnnos |
Man page
Source code
|
| getExprs |
Man page
Source code
|
| get_exprs |
Man page
Man page
|
| get_exprs,SCESet-method |
Man page
Man page
|
| get_exprs.SCESet |
Man page
Source code
|
| isOutlier |
Man page
Source code
|
| isSpike |
Man page
Man page
|
| isSpike,SCESet-method |
Man page
|
| is_exprs |
Man page
Man page
|
| is_exprs,SCESet-method |
Man page
Man page
|
| is_exprs.SCESet |
Man page
Source code
|
| is_exprs<- |
Man page
Man page
|
| is_exprs<-,SCESet,matrix-method |
Man page
|
| mergeSCESet |
Man page
Source code
|
| multiplot |
Man page
Source code
|
| mutate |
Man page
Man page
|
| mutate,SCESet-method |
Man page
Man page
|
| mutate.SCESet |
Man page
Source code
|
| newSCESet |
Man page
Source code
|
| nexprs |
Man page
Source code
|
| norm_counts |
Man page
Man page
Man page
|
| norm_counts,SCESet-method |
Man page
Man page
|
| norm_counts.SCESet |
Man page
Source code
|
| norm_counts<- |
Man page
|
| norm_counts<-,SCESet,matrix-method |
Man page
|
| norm_cpm |
Man page
Man page
Man page
|
| norm_cpm,SCESet-method |
Man page
Man page
|
| norm_cpm.SCESet |
Man page
Source code
|
| norm_cpm<- |
Man page
Man page
|
| norm_cpm<-,SCESet,matrix-method |
Man page
Man page
|
| norm_exprs |
Man page
Man page
|
| norm_exprs,SCESet-method |
Man page
Man page
|
| norm_exprs.SCESet |
Man page
Source code
|
| norm_exprs<- |
Man page
Man page
|
| norm_exprs<-,SCESet,matrix-method |
Man page
|
| norm_fpkm |
Man page
Man page
Man page
|
| norm_fpkm,SCESet-method |
Man page
Man page
|
| norm_fpkm.SCESet |
Man page
Source code
|
| norm_fpkm<- |
Man page
Man page
|
| norm_fpkm<-,SCESet,matrix-method |
Man page
Man page
|
| norm_tpm |
Man page
Man page
Man page
|
| norm_tpm,SCESet-method |
Man page
Man page
|
| norm_tpm.SCESet |
Man page
Source code
|
| norm_tpm<- |
Man page
Man page
|
| norm_tpm<-,SCESet,matrix-method |
Man page
Man page
|
| normalise |
Man page
Man page
Source code
|
| normalise,SCESet-method |
Man page
|
| normaliseExprs |
Man page
Source code
|
| normalize |
Man page
Man page
|
| normalize,SCESet-method |
Man page
Man page
|
| normalize.SCESet |
Man page
Source code
|
| normalizeExprs |
Man page
Source code
|
| normliseExprs |
Man page
|
| pData |
Man page
Man page
|
| pData,SCESet-method |
Man page
|
| pData<-,SCESet,AnnotatedDataFrame-method |
Man page
|
| pData<-,SCESet,data.frame-method |
Man page
|
| plot |
Man page
Man page
|
| plot,SCESet,ANY-method |
Man page
|
| plot,SCESet-method |
Man page
|
| plotDiffusionMap |
Man page
Man page
Man page
|
| plotDiffusionMap,SCESet-method |
Man page
Man page
|
| plotDiffusionMapSCESet |
Man page
Source code
|
| plotExplanatoryVariables |
Man page
Source code
|
| plotExpression |
Man page
Man page
Man page
Man page
Man page
|
| plotExpression,SCESet-method |
Man page
Man page
|
| plotExpression,data.frame-method |
Man page
Man page
|
| plotExpressionDefault |
Man page
Source code
|
| plotExpressionSCESet |
Man page
Source code
|
| plotExprsFreqVsMean |
Man page
Source code
|
| plotExprsVsTxLength |
Man page
Source code
|
| plotFeatureData |
Man page
Source code
|
| plotHighestExprs |
Man page
Source code
|
| plotMDS |
Man page
Man page
Man page
|
| plotMDS,SCESet-method |
Man page
Man page
|
| plotMDSSCESet |
Man page
Source code
|
| plotMetadata |
Man page
Source code
|
| plotPCA |
Man page
Man page
|
| plotPCA,SCESet-method |
Man page
Man page
|
| plotPCASCESet |
Man page
Source code
|
| plotPhenoData |
Man page
Source code
|
| plotPlatePosition |
Man page
Source code
|
| plotQC |
Man page
Source code
|
| plotRLE |
Man page
Man page
|
| plotRLE,SCESet-method |
Man page
|
| plotReducedDIm |
Man page
|
| plotReducedDim |
Man page
Man page
Man page
Man page
|
| plotReducedDim,SCESet-method |
Man page
Man page
|
| plotReducedDim,data.frame-method |
Man page
Man page
|
| plotReducedDim.SCESet |
Man page
Source code
|
| plotReducedDim.default |
Man page
Source code
|
| plotSCESet |
Man page
Source code
|
| plotTSNE |
Man page
Man page
|
| plotTSNE,SCESet-method |
Man page
|
| read10XResults |
Man page
Source code
|
| readKallistoResults |
Man page
Source code
|
| readKallistoResultsOneSample |
Man page
Source code
|
| readSalmonResults |
Man page
Source code
|
| readSalmonResultsOneSample |
Man page
Source code
|
| readTxResults |
Man page
Source code
|
| redDim |
Man page
|
| redDim,SCESet-method |
Man page
Man page
|
| redDim.SCESet |
Man page
Source code
|
| redDim<- |
Man page
Man page
|
| redDim<-,SCESet,matrix-method |
Man page
|
| reducedDimension |
Man page
Man page
Man page
Man page
Man page
Man page
Man page
|
| reducedDimension,SCESet-method |
Man page
Man page
|
| reducedDimension.SCESet |
Man page
Source code
|
| reducedDimension<- |
Man page
Man page
|
| reducedDimension<-,SCESet,matrix-method |
Man page
|
| rename |
Man page
Man page
|
| rename,SCESet-method |
Man page
Man page
|
| rename.SCESet |
Man page
Source code
|
| runKallisto |
Man page
Source code
|
| runSalmon |
Man page
Source code
|
| sc_example_cell_info |
Man page
|
| sc_example_counts |
Man page
|
| scater_gui |
Man page
Source code
|
| scaterlegacy-package |
Man page
|
| setSpike |
Man page
Man page
|
| setSpike<- |
Man page
|
| setSpike<-,SCESet,NULL-method |
Man page
|
| setSpike<-,SCESet,character-method |
Man page
|
| set_exprs |
Man page
Man page
|
| set_exprs<- |
Man page
|
| set_exprs<-,SCESet,ANY,NULL-method |
Man page
|
| set_exprs<-,SCESet,ANY,matrix-method |
Man page
|
| sizeFactors |
Man page
Man page
|
| sizeFactors,SCESet-method |
Man page
Man page
|
| sizeFactors.SCESet |
Man page
Source code
|
| sizeFactors<- |
Man page
Man page
|
| sizeFactors<-,SCESet,NULL-method |
Man page
Man page
|
| sizeFactors<-,SCESet,numeric-method |
Man page
Man page
|
| spikes |
Man page
Man page
|
| spikes,SCESet-method |
Man page
|
| stand_exprs |
Man page
Man page
|
| stand_exprs,SCESet-method |
Man page
Man page
|
| stand_exprs.SCESet |
Man page
Source code
|
| stand_exprs<- |
Man page
Man page
|
| stand_exprs<-,SCESet,matrix-method |
Man page
|
| summariseExprsAcrossFeatures |
Man page
Source code
|
| toCellDataSet |
Man page
Source code
|
| tpm |
Man page
Man page
Man page
|
| tpm,SCESet-method |
Man page
Man page
|
| tpm.SCESet |
Man page
Source code
|
| tpm<- |
Man page
Man page
|
| tpm<-,SCESet,matrix-method |
Man page
Man page
|
| updateSCESet |
Man page
Source code
|
| whichSpike |
Man page
Man page
|
| whichSpike,SCESet-method |
Man page
|
| writeSCESet |
Man page
Source code
|
