Package: scuttle 1.15.1

Aaron Lun

scuttle: Single-Cell RNA-Seq Analysis Utilities

Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.

Authors:Aaron Lun [aut, cre], Davis McCarthy [aut]

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scuttle.pdf |scuttle.html✨
scuttle/json (API)
NEWS

# Install 'scuttle' in R:
install.packages('scuttle', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

On BioConductor:scuttle-1.15.0(bioc 3.20)scuttle-1.14.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

52 exports 5.74 score 42 dependencies 75 dependents

Last updated 7 days agofrom:2e399c234e

Exports:.assignIndicesToWorkers.bpNotSharedOrUp.guessMinMean.ranksafeQR.splitColsByWorkers.splitRowsByWorkers.splitVectorByWorkers.subset2index.unpackListsaddPerCellQCaddPerCellQCMetricsaddPerFeatureQCaddPerFeatureQCMetricsaggregateAcrossCellsaggregateAcrossFeaturescalculateAveragecalculateCPMcalculateFPKMcalculateTPMcleanSizeFactorscomputeGeometricFactorscomputeLibraryFactorscomputeMedianFactorscomputePooledFactorscomputeSpikeFactorscorrectGroupSummarydownsampleBatchesdownsampleMatrixfitLinearModelgeometricSizeFactorsisOutlierlibrarySizeFactorslogNormCountsmakePerCellDFmakePerFeatureDFmedianSizeFactorsmockSCEnormalizeCountsnumDetectedAcrossCellsnumDetectedAcrossFeaturesoutlier.filterperCellQCFiltersperCellQCMetricsperFeatureQCMetricspooledSizeFactorsquickPerCellQCreadSparseCountssumCountsAcrossCellssumCountsAcrossFeaturessummarizeAssayByGroupuniquifyFeatureNameswhichNonZero

Dependencies:abindaskpassbeachmatBHBiobaseBiocGenericsBiocParallelcodetoolscpp11crayoncurlDelayedArrayDelayedMatrixStatsformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RcppS4ArraysS4VectorsSingleCellExperimentsnowSparseArraysparseMatrixStatsSummarizedExperimentsysUCSC.utilsXVectorzlibbioc

Quality control for single-cell RNA-seq data

Aaron Lun

Rendered fromqc.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2021-02-06
Started: 2021-02-06

Normalizing single-cell RNA-seq data

Aaron Lun

Rendered fromnorm.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2021-02-07
Started: 2021-02-06

Other single-cell RNA-seq analysis utilities

Aaron Lun

Rendered frommisc.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2024-03-05
Started: 2021-02-06

Readme and manuals

Help Manual

Help pageTopics
Add QC metrics to a SummarizedExperimentaddPerCellQC addPerCellQCMetrics addPerFeatureQC addPerFeatureQCMetrics
Aggregate data across groups of cellsaggregateAcrossCells aggregateAcrossCells,SingleCellExperiment-method aggregateAcrossCells,SummarizedExperiment-method
Aggregate feature sets in a SummarizedExperimentaggregateAcrossFeatures
Calculate per-feature average countscalculateAverage calculateAverage,ANY-method calculateAverage,SingleCellExperiment-method calculateAverage,SummarizedExperiment-method
Calculate CPMscalculateCPM calculateCPM,ANY-method calculateCPM,SingleCellExperiment-method calculateCPM,SummarizedExperiment-method
Calculate FPKMscalculateFPKM
Calculate TPMscalculateTPM calculateTPM,ANY-method calculateTPM,SingleCellExperiment-method calculateTPM,SummarizedExperiment-method
Clean out non-positive size factorscleanSizeFactors
Normalization by deconvolutioncomputePooledFactors pooledSizeFactors pooledSizeFactors,ANY-method pooledSizeFactors,SummarizedExperiment-method
Normalization with spike-in countscomputeSpikeFactors
Correct group-level summariescorrectGroupSummary
Downsample batches to equal coveragedownsampleBatches
Downsample a count matrixdownsampleMatrix
Fit a linear modelfitLinearModel
Compute geometric size factorscomputeGeometricFactors geometricSizeFactors geometricSizeFactors,ANY-method geometricSizeFactors,SummarizedExperiment-method
Identify outlier valuesisOutlier outlier.filter outlier.filter-class [.outlier.filter
Compute library size factorscomputeLibraryFactors librarySizeFactors librarySizeFactors,ANY-method librarySizeFactors,SummarizedExperiment-method
Compute log-normalized expression valueslogNormCounts logNormCounts,SingleCellExperiment-method logNormCounts,SummarizedExperiment-method
Create a per-cell data.framemakePerCellDF
Create a per-feature data.framemakePerFeatureDF
Compute median-based size factorscomputeMedianFactors medianSizeFactors medianSizeFactors,ANY-method medianSizeFactors,SummarizedExperiment-method
Mock up a SingleCellExperimentmockSCE
Compute normalized expression valuesnormalizeCounts normalizeCounts,ANY-method normalizeCounts,SingleCellExperiment-method normalizeCounts,SummarizedExperiment-method
Number of detected expression values per group of cellsnumDetectedAcrossCells numDetectedAcrossCells,ANY-method numDetectedAcrossCells,SummarizedExperiment-method
Number of detected expression values per group of featuresnumDetectedAcrossFeatures numDetectedAcrossFeatures,ANY-method numDetectedAcrossFeatures,SummarizedExperiment-method
Compute filters for low-quality cellsperCellQCFilters
Per-cell quality control metricsperCellQCMetrics perCellQCMetrics,ANY-method perCellQCMetrics,SingleCellExperiment-method perCellQCMetrics,SummarizedExperiment-method
Per-feature quality control metricsperFeatureQCMetrics perFeatureQCMetrics,ANY-method perFeatureQCMetrics,SummarizedExperiment-method
Quick cell-level QCquickPerCellQC quickPerCellQC,ANY-method quickPerCellQC,SummarizedExperiment-method
Read sparse count matrix from filereadSparseCounts
Single-cell utilitiesscuttle-pkg
Developer utilities.assignIndicesToWorkers .bpNotSharedOrUp .checkCountMatrix .guessMinMean .ranksafeQR .splitColsByWorkers .splitRowsByWorkers .splitVectorByWorkers .subset2index .unpackLists scuttle-utils
Sum expression across groups of cellssumCountsAcrossCells sumCountsAcrossCells,ANY-method sumCountsAcrossCells,SummarizedExperiment-method
Sum counts across feature setssumCountsAcrossFeatures sumCountsAcrossFeatures,ANY-method sumCountsAcrossFeatures,SummarizedExperiment-method
Summarize an assay by groupsummarizeAssayByGroup summarizeAssayByGroup,ANY-method summarizeAssayByGroup,SummarizedExperiment-method
Make feature names uniqueuniquifyFeatureNames