Various Useful Helper Functions

deseqRes2Tibble | Convert DESeq2 results table into a tibble |

factor2Char | Convert a factor to a character vector, while preserving the... |

factorBreakdown | Break down a factor returning the names of the elements in... |

factorBreakdown.2 | Break down a factor returning the names of the elements in... |

getDataWithCovarianceMatrix | Generates data with covariance structure specified by the... |

getDisplay | Get the display paramters for X11 plotting |

getFactorFromP1rds | Get the colors of a pagoda1 serialised app object as a factor |

getNamedDirectoryListing | Like list.files but return the full path and the vector... |

getParMfrow | get number of rows and cols to use when printing a n.items... |

getSlurmCpus | Get the number of processors allocated to the current job by... |

headtail | Head and tail of a table combined |

is.error | Return TRUE if the parameter is an error object |

ll2a | Convert list of lists of numbers to array |

load.hca.matrix | Load a sparse matrix from an HDF5 file ensuring that the... |

mergeFactor | Merge a previously broken down factor |

mergeMatrices | Merge expression matrices in a list, keeping only common... |

minStringDistance | Find minimum string distance strings in a vector |

mixCellsInMatrix | mix cells in a matrix with a common background profile... |

mixVectorsOnLogical | Generates a new vector from two vectors by combining them... |

NA2FALSE | Convert NA values in x to FALSE |

NA2VALUE | Convert NA values in x to the value specified by val |

namedLevels | Get a vector with the levels of a factor named with their own... |

namedNames | Get a vector of the names of an object named by the names... |

plapply | Parallel apply using the packages parallel, BiocParallel or... |

plotFactorsPercent | Generate a ggplot2 plot comparing two factors for a common... |

randomPositiveDefiniteMatrix | Generates a random positive definite matrix |

read10Xmatrices | read multiple 10x matrices into a single sparse array |

read10xMatrix | Read 10x matrix |

readInDropMatrix | Reads in a data matrix from the in house indrop pipeline |

readKleinMatrix | Reads in an expression matrix as formatted by the Klein lab... |

readMultiple10XmatricesAsList | read multiple 10x matrices and return as a list |

readMultipleInDropMatrices | Reads in multiple indrop matrices |

readMultipleKleinMatrices | Reads in multiple klein matrices and returns them in a list |

removeLevelsBySize | Remove levels and elements from a factor that have fewer than... |

removeLevelsFromFactor | Remove all elements from specificed clusters from a factor... |

replaceClusterFactors | Combine two named factors when the new factor contains a... |

rldpkg | Reload a package from the library |

setDisplay | Set the display parameter for X11 plotting |

sparseMatrixDensity | Get the percent of entries that are filled in a sparse matrix |

str1 | Get the top level structure of an object |

str2 | Get the two top levels of structure of an object |

strpart | Get the specified substring of string delimited by a... |

subSampleCountMatrix | Subsample a count matrix to a specific number of reads |

subSampleCountMatrix2 | Subsample a count matrix to a specific number of reads,... |

symmsetdiff | Get the symmetrical set difference between two sets (XOR) |

tableCorners | get NW, NE, SW and SE corners of a dataframe or matrix |

uniqCombs | Get all unique combinations of elements in a list |

vectorSeqOverlap | Get the number of commong elements among the top n elements... |

writeListOfDFs | Write a list of data.frames as individual csv files |

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