Files in LTLA/scuttle

Single-Cell RNA-Seq Analysis Utilities

R/RcppExports.R R/addPerCellQCMetrics.R R/aggregateAcrossCells.R R/aggregateAcrossFeatures.R R/calculateAverage.R R/calculateCPM.R R/calculateFPKM.R R/calculateTPM.R R/cleanSizeFactors.R R/computeSpikeFactors.R R/correctGroupSummary.R R/downsampleBatches.R R/downsampleMatrix.R R/fitLinearModel.R R/geometricSizeFactors.R R/isOutlier.R R/librarySizeFactors.R R/logNormCounts.R R/makePerCellDF.R R/makePerFeatureDF.R R/medianSizeFactors.R R/mockSCE.R R/normalizeCounts.R R/numDetectedAcrossCells.R R/numDetectedAcrossFeatures.R R/perCellQCFilters.R R/perCellQCMetrics.R R/perFeatureQCMetrics.R R/pooledSizeFactors.R R/quickPerCellQC.R R/readSparseCounts.R R/scuttle-pkg.R R/sumCountsAcrossCells.R R/sumCountsAcrossFeatures.R R/summarizeAssayByGroup.R R/uniquifyDataFrameByGroup.R R/uniquifyFeatureNames.R R/utils_other.R R/utils_parallel.R R/utils_subset.R R/whichNonZero.R man/addPerCellQCMetrics.Rd man/aggregateAcrossCells.Rd man/aggregateAcrossFeatures.Rd man/calculateAverage.Rd man/calculateCPM.Rd man/calculateFPKM.Rd man/calculateTPM.Rd man/cleanSizeFactors.Rd man/computePooledFactors.Rd man/computeSpikeFactors.Rd man/correctGroupSummary.Rd man/downsampleBatches.Rd man/downsampleMatrix.Rd man/fitLinearModel.Rd man/geometricSizeFactors.Rd man/isOutlier.Rd man/librarySizeFactors.Rd man/logNormCounts.Rd man/makePerCellDF.Rd man/makePerFeatureDF.Rd man/medianSizeFactors.Rd man/mockSCE.Rd man/normalizeCounts.Rd man/numDetectedAcrossCells.Rd man/numDetectedAcrossFeatures.Rd man/perCellQCFilters.Rd man/perCellQCMetrics.Rd man/perFeatureQCMetrics.Rd man/quickPerCellQC.Rd man/readSparseCounts.Rd man/reexports.Rd man/scuttle-pkg.Rd man/scuttle-utils.Rd man/sumCountsAcrossCells.Rd man/sumCountsAcrossFeatures.Rd man/summarizeAssayByGroup.Rd man/uniquifyDataFrameByGroup.Rd man/uniquifyFeatureNames.Rd tests/testthat.R tests/testthat/setup.R tests/testthat/test-calc-ave.R tests/testthat/test-calc-cpm.R tests/testthat/test-clean-size-factors.R tests/testthat/test-correct-summary.R tests/testthat/test-downsample.R tests/testthat/test-feat-proc.R tests/testthat/test-linear-model.R tests/testthat/test-load-data.R tests/testthat/test-make-df.R tests/testthat/test-norm.R tests/testthat/test-pool-size-factors.R tests/testthat/test-qc-calc.R tests/testthat/test-qc-filters.R tests/testthat/test-qc-outlier.R tests/testthat/test-size-factors.R tests/testthat/test-spike-size-factors.R tests/testthat/test-sum-across-cells.R tests/testthat/test-sum-across-feat.R tests/testthat/test-utils.R vignettes/misc.Rmd vignettes/norm.Rmd vignettes/qc.Rmd