LTLA/scuttle
Single-Cell RNA-Seq Analysis Utilities

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190
Source code
61
Man pages
37
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LTLA/scuttle: Single-Cell RNA-Seq Analysis Utilities
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API

API for LTLA/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_pooled_factors Source code
.calculate_tpm Source code
.cbind_empty Source code
.center.size.factors Source code
.checkCountMatrix Man page
.check_methods Source code
.choose_transform Source code
.create_coldata Source code
.create_linear_system Source code
.determine_sharingness Source code
.df_to_factor Source code
.downsample_counts Source code
.empty_df_from_se Source code
.flatten_nested_dims Source code
.generateSphere Source code
.geometric_size_factors Source code
.get_default_sizes Source code
.get_med_and_mad Source code
.guessMinMean Man page Source code
.harvest_se_by_column Source code
.has_multi_ids Source code
.library_size_factors Source code
.limit_cluster_size 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_cluster_normalize Source code
.per_feature_qc Source code
.per_feature_qc_metrics Source code
.process_ids Source code
.ranksafeQR Man page Source code
.replace Source code
.rescale_clusters 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
[.outlier.filter Man page
`[.outlier.filter` Source code
addPerCellQC Man page
addPerCellQCMetrics Man page Source code
addPerFeatureQC Man page
addPerFeatureQCMetrics 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
cleanSizeFactors Man page Source code
computeGeometricFactors Man page Source code
computeLibraryFactors Man page Source code
computeMedianFactors Man page Source code
computePooledFactors Man page Source code
computeSpikeFactors Man page Source code
correctGroupSummary 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
outlier.filter Man page Source code
outlier.filter-class Man page
perCellQCFilters Man page Source code
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
pool_size_factors Source code
pooledSizeFactors Man page
pooledSizeFactors,ANY-method Man page
pooledSizeFactors,SummarizedExperiment-method Man page
quickPerCellQC Man page
quickPerCellQC,ANY-method Man page
quickPerCellQC,SummarizedExperiment-method Man page
readSparseCounts Man page Source code
reexports Man page
scuttle-pkg Man page
scuttle-utils Man page
sparse_aggregate_detected Source code
sparse_aggregate_sum Source code
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
LTLA/scuttle documentation built on March 9, 2024, 11:16 a.m.

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