Package: scuttle 1.22.0
Aaron Lun
scuttle: Legacy Utilities for Single-Cell RNA-Seq Analysis
Provides some legacy utility functions for performing single-cell analyses. Most of these functions are deprecated in favor of newer, more performant alternatives. We just keep this package around for back-compatibility and to point to the replacement functions.
Authors:
scuttle_1.22.0.tar.gz
scuttle_1.22.0.zip(r-4.7)scuttle_1.22.0.zip(r-4.6)scuttle_1.22.0.zip(r-4.5)
scuttle_1.22.0.tgz(r-4.6-x86_64)scuttle_1.22.0.tgz(r-4.6-arm64)scuttle_1.22.0.tgz(r-4.5-x86_64)scuttle_1.22.0.tgz(r-4.5-arm64)
scuttle_1.22.0.tar.gz(r-4.7-arm64)scuttle_1.22.0.tar.gz(r-4.7-x86_64)scuttle_1.22.0.tar.gz(r-4.6-arm64)scuttle_1.22.0.tar.gz(r-4.6-x86_64)
scuttle_1.22.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scuttle/json (API)
NEWS
| # Install 'scuttle' in R: |
| install.packages('scuttle', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:scuttle-1.23.1(bioc 3.24)scuttle-1.22.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysinglecellrnaseqqualitycontrolpreprocessingnormalizationtranscriptomicsgeneexpressionsequencingsoftwaredataimportopenblascpp
Last updated from:d56a81e414 (on RELEASE_3_23). Checks:12 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 267 | ||
| linux-devel-arm64 | WARNING | 404 | ||
| linux-devel-x86_64 | WARNING | 465 | ||
| source / vignettes | OK | 548 | ||
| linux-release-arm64 | WARNING | 436 | ||
| linux-release-x86_64 | WARNING | 509 | ||
| macos-release-arm64 | WARNING | 465 | ||
| macos-release-x86_64 | WARNING | 445 | ||
| macos-oldrel-arm64 | WARNING | 344 | ||
| macos-oldrel-x86_64 | WARNING | 669 | ||
| windows-devel | WARNING | 1643 | ||
| windows-release | WARNING | 1848 | ||
| windows-oldrel | WARNING | 1939 | ||
| wasm-release | OK | 213 |
Exports:.assignIndicesToWorkers.bpNotSharedOrUp.guessMinMean.ranksafeQR.splitColsByWorkers.splitRowsByWorkers.splitVectorByWorkers.subset2index.unpackListsaddPerCellQCaddPerCellQCMetricsaddPerFeatureQCaddPerFeatureQCMetricsaggregateAcrossCellsaggregateAcrossFeaturescalculateAveragecalculateCPMcalculateFPKMcalculateTPMcleanSizeFactorscomputeGeometricFactorscomputeLibraryFactorscomputeMedianFactorscomputePooledFactorscomputeSpikeFactorscorrectGroupSummarydownsampleBatchesdownsampleMatrixfitLinearModelgeometricSizeFactorsisOutlierlibrarySizeFactorslogNormCountsmakePerCellDFmakePerFeatureDFmedianSizeFactorsmockSCEnormalizeCountsnumDetectedAcrossCellsnumDetectedAcrossFeaturesoutlier.filterperCellQCFiltersperCellQCMetricsperFeatureQCMetricspooledSizeFactorsquickPerCellQCreadSparseCountssumCountsAcrossCellssumCountsAcrossFeaturessummarizeAssayByGroupuniquifyDataFrameByGroupuniquifyFeatureNameswhichNonZero
Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocParallelcodetoolscpp11DelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicRangesIRangeslambda.rlatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSeqinfoSingleCellExperimentsnowSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add QC metrics to a SummarizedExperiment | addPerCellQC addPerCellQCMetrics addPerFeatureQC addPerFeatureQCMetrics |
| Aggregate data across groups of cells | aggregateAcrossCells aggregateAcrossCells,SingleCellExperiment-method aggregateAcrossCells,SummarizedExperiment-method |
| Aggregate feature sets in a SummarizedExperiment | aggregateAcrossFeatures |
| Calculate per-feature average counts | calculateAverage calculateAverage,ANY-method calculateAverage,SingleCellExperiment-method calculateAverage,SummarizedExperiment-method |
| Calculate CPMs | calculateCPM calculateCPM,ANY-method calculateCPM,SingleCellExperiment-method calculateCPM,SummarizedExperiment-method |
| Calculate FPKMs | calculateFPKM |
| Calculate TPMs | calculateTPM calculateTPM,ANY-method calculateTPM,SingleCellExperiment-method calculateTPM,SummarizedExperiment-method |
| Clean out non-positive size factors | cleanSizeFactors |
| Normalization by deconvolution | computePooledFactors pooledSizeFactors pooledSizeFactors,ANY-method pooledSizeFactors,SummarizedExperiment-method |
| Normalization with spike-in counts | computeSpikeFactors |
| Correct group-level summaries | correctGroupSummary |
| Downsample batches to equal coverage | downsampleBatches |
| Downsample a count matrix | downsampleMatrix |
| Fit a linear model | fitLinearModel |
| Compute geometric size factors | computeGeometricFactors geometricSizeFactors geometricSizeFactors,ANY-method geometricSizeFactors,SummarizedExperiment-method |
| Identify outlier values | isOutlier outlier.filter outlier.filter-class [.outlier.filter |
| Compute library size factors | computeLibraryFactors librarySizeFactors librarySizeFactors,ANY-method librarySizeFactors,SummarizedExperiment-method |
| Compute log-normalized expression values | logNormCounts logNormCounts,SingleCellExperiment-method logNormCounts,SummarizedExperiment-method |
| Create a per-cell data.frame | makePerCellDF |
| Create a per-feature data.frame | makePerFeatureDF |
| Compute median-based size factors | computeMedianFactors medianSizeFactors medianSizeFactors,ANY-method medianSizeFactors,SummarizedExperiment-method |
| Mock up a SingleCellExperiment | mockSCE |
| Compute normalized expression values | normalizeCounts normalizeCounts,ANY-method normalizeCounts,SingleCellExperiment-method normalizeCounts,SummarizedExperiment-method |
| Number of detected expression values per group of cells | numDetectedAcrossCells numDetectedAcrossCells,ANY-method numDetectedAcrossCells,SummarizedExperiment-method |
| Number of detected expression values per group of features | numDetectedAcrossFeatures numDetectedAcrossFeatures,ANY-method numDetectedAcrossFeatures,SummarizedExperiment-method |
| Compute filters for low-quality cells | perCellQCFilters |
| Per-cell quality control metrics | perCellQCMetrics perCellQCMetrics,ANY-method perCellQCMetrics,SingleCellExperiment-method perCellQCMetrics,SummarizedExperiment-method |
| Per-feature quality control metrics | perFeatureQCMetrics perFeatureQCMetrics,ANY-method perFeatureQCMetrics,SummarizedExperiment-method |
| Quick cell-level QC | quickPerCellQC quickPerCellQC,ANY-method quickPerCellQC,SummarizedExperiment-method |
| Read sparse count matrix from file | readSparseCounts |
| Single-cell utilities | scuttle-pkg |
| Developer utilities | .assignIndicesToWorkers .bpNotSharedOrUp .checkCountMatrix .guessMinMean .ranksafeQR .splitColsByWorkers .splitRowsByWorkers .splitVectorByWorkers .subset2index .unpackLists scuttle-utils |
| Sum expression across groups of cells | sumCountsAcrossCells sumCountsAcrossCells,ANY-method sumCountsAcrossCells,SummarizedExperiment-method |
| Sum counts across feature sets | sumCountsAcrossFeatures sumCountsAcrossFeatures,ANY-method sumCountsAcrossFeatures,SummarizedExperiment-method |
| Summarize an assay by group | summarizeAssayByGroup summarizeAssayByGroup,ANY-method summarizeAssayByGroup,SummarizedExperiment-method |
| Groupwise unique rows of a DataFrame | uniquifyDataFrameByGroup |
| Make feature names unique | uniquifyFeatureNames |
