Single-Cell RNA-Seq Analysis Utilities

addPerCellQC | Add QC metrics to a SummarizedExperiment |

aggregateAcrossCells | Aggregate data across groups of cells |

aggregateAcrossFeatures | Aggregate feature sets in a SummarizedExperiment |

calculateAverage | Calculate per-feature average counts |

calculateCPM | Calculate CPMs |

calculateFPKM | Calculate FPKMs |

calculateTPM | Calculate TPMs |

downsampleBatches | Downsample batches to equal coverage |

downsampleMatrix | Downsample a count matrix |

fitLinearModel | Fit a linear model |

geometricSizeFactors | Compute geometric size factors |

isOutlier | Identify outlier values |

librarySizeFactors | Compute library size factors |

logNormCounts | Compute log-normalized expression values |

makePerCellDF | Create a per-cell data.frame |

makePerFeatureDF | Create a per-feature data.frame |

medianSizeFactors | Compute median-based size factors |

mockSCE | Mock up a SingleCellExperiment |

normalizeCounts | Compute normalized expression values |

numDetectedAcrossCells | Number of detected expression values per group of cells |

numDetectedAcrossFeatures | Number of detected expression values per group of features |

perCellQCMetrics | Per-cell quality control metrics |

perFeatureQCMetrics | Per-feature quality control metrics |

quickPerCellQC | Quick cell-level QC |

readSparseCounts | Read sparse count matrix from file |

scuttle-pkg | Single-cell utilities |

scuttle-utils | Developer utilities |

sumCountsAcrossCells | Sum expression across groups of cells |

sumCountsAcrossFeatures | Sum counts across feature sets |

summarizeAssayByGroup | Summarize an assay by group |

uniquifyFeatureNames | Make feature names unique |

whichNonZero | Find non-zero entries of a matrix |

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