Fishpond: downstream methods and tools for expression data

addStatsFromCSV | Read statistics and nulls from CSV file |

alevinEC | Construct a sparse matrix of transcript compatibility counts... |

computeInfRV | Compute inferential relative variance (InfRV) |

deswish | deswish: DESeq2-apeglm With Inferential Samples Helps |

fishpond-package | Fishpond: downstream methods and tools for expression data |

getTrace | Obtain a trace of inferential replicates for a sample |

importAllelicCounts | Import allelic counts as a SummarizedExperiment |

isoformProportions | Create isoform proportions from scaled data |

labelKeep | Label rows to keep based on minimal count |

loadFry | Load in data from alevin-fry USA mode |

makeInfReps | Make pseudo-inferential replicates from mean and variance |

makeSimSwishData | Make simulated data for swish for examples/testing |

makeTx2Tss | Make a GRanges linking transcripts to TSS within gene |

miniSwish | Helper function for distributing Swish on a subset of data |

plotAllelicGene | Plot allelic counts in a gene context using Gviz |

plotAllelicHeatmap | Plot allelic ratio heatmap |

plotInfReps | Plot inferential replicates for a gene or transcript |

plotMASwish | MA plot - log fold change over average counts |

salmonEC | Construct a sparse matrix of transcript compatibility counts... |

scaleInfReps | Scale inferential replicate counts |

splitSwish | Function for splitting SummarizedExperiment into separate RDS... |

swish | Swish method: differential expression accounting for... |

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