A B C F G I M N P R S T U W misc
scater-package | Single-cell analysis toolkit for expression in R |
arrange | Arrange rows of 'pData(object)' by variables. |
arrange-method | Arrange rows of 'pData(object)' by variables. |
arrange.SCESet | Arrange rows of 'pData(object)' by variables. |
bootstraps | Accessor and replacement for bootstrap results in an SCESet object |
bootstraps-method | Accessor and replacement for bootstrap results in an SCESet object |
bootstraps.SCESet | Accessor and replacement for bootstrap results in an SCESet object |
bootstraps<- | Accessor and replacement for bootstrap results in an SCESet object |
bootstraps<--method | Accessor and replacement for bootstrap results in an SCESet object |
calcIsExprs | Calculate which features are expressed in which cells using a threshold on observed counts, transcripts-per-million, counts-per-million, FPKM, or defined expression levels. |
calculateFPKM | Calculate fragments per kilobase of exon per million reads mapped (FPKM) |
calculateQCMetrics | Calculate QC metrics |
calculateTPM | Calculate transcripts-per-million (TPM) |
cellDist | cellPairwiseDistances in an SCESet object |
cellDist-method | cellPairwiseDistances in an SCESet object |
cellDist<- | cellPairwiseDistances in an SCESet object |
cellDist<--method | cellPairwiseDistances in an SCESet object |
cellDistSCESet | cellPairwiseDistances in an SCESet object |
cellNames | Get or set cell names from an SCESet object |
cellNames<- | Get or set cell names from an SCESet object |
cellNames<--method | Get or set cell names from an SCESet object |
cellPairwiseDistances | cellPairwiseDistances in an SCESet object |
cellPairwiseDistances-method | cellPairwiseDistances in an SCESet object |
cellPairwiseDistances.SCESet | cellPairwiseDistances in an SCESet object |
cellPairwiseDistances<- | cellPairwiseDistances in an SCESet object |
cellPairwiseDistances<--method | cellPairwiseDistances in an SCESet object |
counts | Accessors for the 'counts' element of an SCESet object. |
counts-method | Accessors for the 'counts' element of an SCESet object. |
counts.SCESet | Accessors for the 'counts' element of an SCESet object. |
counts<--method | Accessors for the 'counts' element of an SCESet object. |
cpm | Accessors for the 'cpm' (counts per million) element of an SCESet object. |
cpm-method | Accessors for the 'cpm' (counts per million) element of an SCESet object. |
cpm<- | Accessors for the 'cpm' (counts per million) element of an SCESet object. |
cpm<--method | Accessors for the 'cpm' (counts per million) element of an SCESet object. |
cpmSCESet | Accessors for the 'cpm' (counts per million) element of an SCESet object. |
fData | Replaces featureData in an SCESet object |
fData-method | Replaces featureData in an SCESet object |
fData<--method | Replaces featureData in an SCESet object |
featDist | featurePairwiseDistances in an SCESet object |
featDist-method | featurePairwiseDistances in an SCESet object |
featDist<- | featurePairwiseDistances in an SCESet object |
featDist<--method | featurePairwiseDistances in an SCESet object |
featDistSCESet | featurePairwiseDistances in an SCESet object |
featurePairwiseDistances | featurePairwiseDistances in an SCESet object |
featurePairwiseDistances-method | featurePairwiseDistances in an SCESet object |
featurePairwiseDistances<- | featurePairwiseDistances in an SCESet object |
featurePairwiseDistances<--method | featurePairwiseDistances in an SCESet object |
featurePairwiseDistancesSCESet | featurePairwiseDistances in an SCESet object |
filter | Return 'SCESet' with cells matching conditions. |
filter-method | Return 'SCESet' with cells matching conditions. |
filter.SCESet | Return 'SCESet' with cells matching conditions. |
findImportantPCs | Find most important principal components for a given variable |
fpkm | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
fpkm-method | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
fpkm.SCESet | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
fpkm<- | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
fpkm<--method | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
fromCellDataSet | Convert a 'CellDataSet' to an 'SCESet' |
getBMFeatureAnnos | Get feature annotation information from Biomart |
getExprs | Retrieve a representation of gene expression |
get_exprs | Generic accessor for expression data from an SCESet object. |
get_exprs-method | Generic accessor for expression data from an SCESet object. |
get_exprs.SCESet | Generic accessor for expression data from an SCESet object. |
isOutlier | Identify if a cell is an outlier based on a metric |
is_exprs | Accessors for the 'is_exprs' element of an SCESet object. |
is_exprs-method | Accessors for the 'is_exprs' element of an SCESet object. |
is_exprs.SCESet | Accessors for the 'is_exprs' element of an SCESet object. |
is_exprs<- | Accessors for the 'is_exprs' element of an SCESet object. |
is_exprs<--method | Accessors for the 'is_exprs' element of an SCESet object. |
mergeSCESet | Merge SCESet objects |
multiplot | Multiple plot function for ggplot2 plots |
mutate | Add new variables to 'pData(object)'. |
mutate-method | Add new variables to 'pData(object)'. |
mutate.SCESet | Add new variables to 'pData(object)'. |
newSCESet | Create a new SCESet object. |
nexprs | Count the number of expressed genes per cell |
normalise | Normalise an SCESet object using pre-computed size factors |
normalise-method | Normalise an SCESet object using pre-computed size factors |
normaliseExprs | Normalise expression expression levels for an SCESet object |
normalize | Normalise an SCESet object using pre-computed size factors |
normalize-method | Normalise an SCESet object using pre-computed size factors |
normalize.SCESet | Normalise an SCESet object using pre-computed size factors |
normalizeExprs | Normalise expression expression levels for an SCESet object |
normliseExprs | Normalise expression expression levels for an SCESet object |
norm_counts | Accessors for the 'norm_counts' element of an SCESet object. |
norm_counts-method | Accessors for the 'norm_counts' element of an SCESet object. |
norm_counts.SCESet | Accessors for the 'norm_counts' element of an SCESet object. |
norm_counts<- | Accessors for the 'norm_counts' element of an SCESet object. |
norm_counts<--method | Accessors for the 'norm_counts' element of an SCESet object. |
norm_cpm | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object. |
norm_cpm-method | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object. |
norm_cpm.SCESet | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object. |
norm_cpm<- | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object. |
norm_cpm<--method | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object. |
norm_exprs | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object. |
norm_exprs-method | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object. |
norm_exprs.SCESet | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object. |
norm_exprs<- | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object. |
norm_exprs<--method | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object. |
norm_fpkm | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
norm_fpkm-method | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
norm_fpkm.SCESet | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
norm_fpkm<- | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
norm_fpkm<--method | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
norm_tpm | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object. |
norm_tpm-method | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object. |
norm_tpm.SCESet | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object. |
norm_tpm<- | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object. |
norm_tpm<--method | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object. |
pData | Replaces phenoData in an SCESet object |
pData-method | Replaces phenoData in an SCESet object |
pData<--method | Replaces phenoData in an SCESet object |
plot | Plot an overview of expression for each cell |
plot-method | Plot an overview of expression for each cell |
plotDiffusionMap | Plot a diffusion map for an SCESet object |
plotDiffusionMap-method | Plot a diffusion map for an SCESet object |
plotDiffusionMapSCESet | Plot a diffusion map for an SCESet object |
plotExplanatoryVariables | Plot explanatory variables ordered by percentage of phenotypic variance explained |
plotExpression | Plot expression values for a set of features (e.g. genes or transcripts) |
plotExpression-method | Plot expression values for a set of features (e.g. genes or transcripts) |
plotExpressionDefault | Plot expression values for a set of features (e.g. genes or transcripts) |
plotExpressionSCESet | Plot expression values for a set of features (e.g. genes or transcripts) |
plotExprsFreqVsMean | Plot frequency of expression against mean expression level |
plotExprsVsTxLength | Plot expression against transcript length |
plotFeatureData | Plot feature (gene) data from an SCESet object |
plotHighestExprs | Plot the features with the highest expression values |
plotMDS | Produce a multidimensional scaling plot for an SCESet object |
plotMDS-method | Produce a multidimensional scaling plot for an SCESet object |
plotMDSSCESet | Produce a multidimensional scaling plot for an SCESet object |
plotMetadata | Plot metadata for cells or features |
plotPCA | Plot PCA for an SCESet object |
plotPCA-method | Plot PCA for an SCESet object |
plotPCASCESet | Plot PCA for an SCESet object |
plotPhenoData | Plot phenotype data from an SCESet object |
plotPlatePosition | Plot cells in plate positions |
plotQC | Produce QC diagnostic plots |
plotReducedDIm | Plot reduced dimension representation of cells |
plotReducedDim | Plot reduced dimension representation of cells |
plotReducedDim-method | Plot reduced dimension representation of cells |
plotReducedDim.default | Plot reduced dimension representation of cells |
plotReducedDim.SCESet | Plot reduced dimension representation of cells |
plotSCESet | Plot an overview of expression for each cell |
plotTSNE | Plot t-SNE for an SCESet object |
plotTSNE-method | Plot t-SNE for an SCESet object |
readKallistoResults | Read kallisto results from a batch of jobs |
readKallistoResultsOneSample | Read kallisto results for a single sample into a list |
readSalmonResults | Read Salmon results from a batch of jobs |
readSalmonResultsOneSample | Read Salmon results for a single sample into a list |
readTxResults | Read transcript quantification data with tximport package |
redDim | Reduced dimension representation for cells in an SCESet object |
redDim-method | Reduced dimension representation for cells in an SCESet object |
redDim.SCESet | Reduced dimension representation for cells in an SCESet object |
redDim<- | Reduced dimension representation for cells in an SCESet object |
redDim<--method | Reduced dimension representation for cells in an SCESet object |
reducedDimension | Reduced dimension representation for cells in an SCESet object |
reducedDimension-method | Reduced dimension representation for cells in an SCESet object |
reducedDimension.SCESet | Reduced dimension representation for cells in an SCESet object |
reducedDimension<- | Reduced dimension representation for cells in an SCESet object |
reducedDimension<--method | Reduced dimension representation for cells in an SCESet object |
rename | Rename variables of 'pData(object)'. |
rename-method | Rename variables of 'pData(object)'. |
rename.SCESet | Rename variables of 'pData(object)'. |
runKallisto | Run kallisto on FASTQ files to quantify feature abundance |
runSalmon | Run Salmon on FASTQ files to quantify feature abundance |
scater_gui | scater GUI function |
SCESet | The "Single Cell Expression Set" (SCESet) class |
SCESet-class | The "Single Cell Expression Set" (SCESet) class |
SCESet-subset | Subsetting SCESet Objects |
sc_example_cell_info | Cell information for the small example single-cell counts dataset to demonstrate capabilities of scater |
sc_example_counts | A small example of single-cell counts dataset to demonstrate capabilities of scater |
set_exprs | Assignment method for the new elements of an SCESet object. |
set_exprs<- | Assignment method for the new elements of an SCESet object. |
set_exprs<--method | Assignment method for the new elements of an SCESet object. |
sizeFactors | Accessors size factors of an SCESet object. |
sizeFactors-method | Accessors size factors of an SCESet object. |
sizeFactors.SCESet | Accessors size factors of an SCESet object. |
sizeFactors<- | Accessors size factors of an SCESet object. |
sizeFactors<--method | Accessors size factors of an SCESet object. |
stand_exprs | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object. |
stand_exprs-method | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object. |
stand_exprs.SCESet | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object. |
stand_exprs<- | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object. |
stand_exprs<--method | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object. |
summariseExprsAcrossFeatures | Summarise expression values across feature |
toCellDataSet | Convert an 'SCESet' to a 'CellDataSet' |
tpm | Accessors for the 'tpm' (transcripts per million) element of an SCESet object. |
tpm-method | Accessors for the 'tpm' (transcripts per million) element of an SCESet object. |
tpm.SCESet | Accessors for the 'tpm' (transcripts per million) element of an SCESet object. |
tpm<- | Accessors for the 'tpm' (transcripts per million) element of an SCESet object. |
tpm<--method | Accessors for the 'tpm' (transcripts per million) element of an SCESet object. |
updateSCESet | Update an SCESet object to the current version |
writeSCESet | Write an SCESet object to an HDF5 file |
[-method | Subsetting SCESet Objects |