scuttle
Single-Cell RNA-Seq Analysis Utilities

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159
Source code
54
Man pages
32
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API

API for scuttle
Single-Cell RNA-Seq Analysis Utilities

Global functions
.apply_filters Source code
.apply_suffixes Source code
.assignIndicesToWorkers Man page Source code
.average2statistic Source code
.bpNotSharedOrUp Man page Source code
.calculate_average Source code
.calculate_cpm Source code
.calculate_tpm Source code
.cbind_empty Source code
.center.size.factors Source code
.checkCountMatrix Man page
.create_coldata Source code
.determine_sharingness Source code
.df_to_factor Source code
.downsample_counts Source code
.flatten_nested_dims Source code
.geometric_size_factors Source code
.get_default_sizes Source code
.get_med_and_mad Source code
.harvest_se_by_column Source code
.has_multi_ids Source code
.library_size_factors Source code
.median_size_factors Source code
.merge_DF_rows Source code
.multi_object_downsample Source code
.nexprs_across_cells Source code
.nexprs_across_features Source code
.noOpSubset Source code
.per_cell_qc Source code
.per_cell_qc_metrics Source code
.per_feature_qc Source code
.per_feature_qc_metrics Source code
.process_ids Source code
.quickPerCellQC Source code
.ranksafeQR Man page Source code
.replace Source code
.se_lnc Source code
.single_object_downsample Source code
.single_worker_matrix Source code
.splitColsByWorkers Man page Source code
.splitRowsByWorkers Man page Source code
.splitVectorByWorkers Man page Source code
.subset2index Man page Source code
.sum_across_features Source code
.sum_counts_across_cells Source code
.sum_counts_across_features Source code
.summarize_assay Source code
.summarize_assay_by_group Source code
.summarize_assay_internal Source code
.transform_sparse Source code
.unpackLists Man page Source code
.use_names_to_integer_indices Source code
addPerCellQC Man page Source code
addPerFeatureQC Man page Source code
aggregateAcrossCells Man page
aggregateAcrossCells,SingleCellExperiment-method Man page
aggregateAcrossCells,SummarizedExperiment-method Man page
aggregateAcrossFeatures Man page Source code
calculateAverage Man page
calculateAverage,ANY-method Man page
calculateAverage,SingleCellExperiment-method Man page
calculateAverage,SummarizedExperiment-method Man page
calculateCPM Man page
calculateCPM,ANY-method Man page
calculateCPM,SingleCellExperiment-method Man page
calculateCPM,SummarizedExperiment-method Man page
calculateFPKM Man page Source code
calculateTPM Man page
calculateTPM,ANY-method Man page
calculateTPM,SingleCellExperiment-method Man page
calculateTPM,SummarizedExperiment-method Man page
computeGeometricFactors Man page Source code
computeLibraryFactors Man page Source code
computeMedianFactors Man page Source code
cumulative_prop Source code
downsampleBatches Man page Source code
downsampleMatrix Man page Source code
downsample_column Source code
downsample_matrix Source code
fitLinearModel Man page Source code
fit_linear_model Source code
geometricSizeFactors Man page
geometricSizeFactors,ANY-method Man page
geometricSizeFactors,SummarizedExperiment-method Man page
isOutlier Man page Source code
librarySizeFactors Man page
librarySizeFactors,ANY-method Man page
librarySizeFactors,SummarizedExperiment-method Man page
logNormCounts Man page
logNormCounts,SingleCellExperiment-method Man page
logNormCounts,SummarizedExperiment-method Man page
makePerCellDF Man page Source code
makePerFeatureDF Man page Source code
medianSizeFactors Man page
medianSizeFactors,ANY-method Man page
medianSizeFactors,SummarizedExperiment-method Man page
mockSCE Man page Source code
normalizeCounts Man page
normalizeCounts,ANY-method Man page
normalizeCounts,SingleCellExperiment-method Man page
normalizeCounts,SummarizedExperiment-method Man page
numDetectedAcrossCells Man page
numDetectedAcrossCells,ANY-method Man page
numDetectedAcrossCells,SummarizedExperiment-method Man page
numDetectedAcrossFeatures Man page
numDetectedAcrossFeatures,ANY-method Man page
numDetectedAcrossFeatures,SummarizedExperiment-method Man page
perCellQCMetrics Man page
perCellQCMetrics,ANY-method Man page
perCellQCMetrics,SingleCellExperiment-method Man page
perCellQCMetrics,SummarizedExperiment-method Man page
perFeatureQCMetrics Man page
perFeatureQCMetrics,ANY-method Man page
perFeatureQCMetrics,SummarizedExperiment-method Man page
quickPerCellQC Man page
quickPerCellQC,ANY-method Man page
quickPerCellQC,SummarizedExperiment-method Man page
readSparseCounts Man page Source code
scuttle-pkg Man page
scuttle-utils Man page
sumCountsAcrossCells Man page
sumCountsAcrossCells,ANY-method Man page
sumCountsAcrossCells,SummarizedExperiment-method Man page
sumCountsAcrossFeatures Man page
sumCountsAcrossFeatures,ANY-method Man page
sumCountsAcrossFeatures,SummarizedExperiment-method Man page
sum_row_counts Source code
summarizeAssayByGroup Man page
summarizeAssayByGroup,ANY-method Man page
summarizeAssayByGroup,SummarizedExperiment-method Man page
uniquifyFeatureNames Man page Source code
whichNonZero Man page
whichNonZero,ANY-method Man page
whichNonZero,dgCMatrix-method Man page
whichNonZero,dgTMatrix-method Man page
scuttle documentation built on Dec. 19, 2020, 2 a.m.

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