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 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' |
newSCESet |
Create a new SCESet object. |
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. |
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 |