Changes in version 2.2.4 Increased reliability of clustering functions by improved error handling and by allowing retry runs on estimators functions Speed-up of GDI calculation via Rfast package Changes in version 2.2.3 Solved issue with cleanPlots() when the number of cells exceeded 65536 Changes in version 2.2.2 Stopped using explicit PCA via irlba package: using BioConductor PCAtools::pca() instead Changes in version 2.2.1 Fixed minor issue with test on MacOS on arm64 architectures Changes in version 2.2.0 Produced new version 2.2.0 for BioConductor 3.18 Changes in version 2.1.8 Made passing clusterizations to COTAN functions more easy: now all functions that take a COTAN object and a clusterization as input parameters can also take a clusterization name Added time-stamps to log entries when written on a log file Fixed bug in the clustersMarkersHeatmapPlot function when given a clusterization not matching the latest added to the COTAN object Fixed issue with the highest possible resolution in seuratClustering() function, needed when large datasets must be split in many clusters Changes in version 2.1.7 Added new flag to the function cleanPlots() to suppress evaluation of the PCA on the normalized data. In particular, this allows to reduce significantly time spent within the function checkClusterUniformity() Added initialResolution parameter to cellsUniformClustering(): it allows users to specify the initial resolution used in the calls to Seurat::FindClusters() method. It now uses the same default as Seurat Added new method estimateNuLinearByCluster() that calculates nu ensuring that its average is 1.0 in each given cluster Changes in version 2.1.6 Added function reorderClusterization(): it reorders the given clusterization so that near clusters have also near labels The functions cellsUniformClustering() and mergeUniformCellsClusters() now return the result of this new function Separated p-value calculations from DEAOnClusters() into the new function pValueFromDEA(). Those data.frames are no longer part of the list returned by the functions DEAOnClusters() and mergeUniformCellsClusters() Added function getClusters() to retrieve the wanted clusterization from the cells' meta-dataset Added function calculateGenesCE(): it returns the cross-entropy between the expected absence of a gene reading against the observed state Fixed minor issue with logThis() to file: it was always appending a new line even when appendLF was set to FALSE Now checkClusterUniformity() returns more GDI stats like the percentage of genes above threshold or the last percentile of the GDI values Revamped mergeUniformCellsClusters() to select in order all the the most likely candidates pairs of clusters to merge. Provided new user parameter to balance the merging of most possible candidates versus the time spent doing so Improved dropGenesCells() method: it now retains all meta-data information that is not related to the results of the other methods Added zoomed UDE plot to cleanPlots() return. It suggests a possible cut level for low UDE cells Changes in version 2.1.5 Improved mergeUniformCellsClusters(): now it attempts to merge more clusters pairs Now errors in the seuratClustering() function are interpreted as remaining cells not-clustered "-1". This applies mostly to cases when Seurat finds only singlets Added flag calcCoex to proceedToCoex() and automaticCOTANObjectCreation() functions to allow user not to spend time calculating the genes' COEX when not needed Solved potential issue in the clustersMarkersHeatmapPlot() regarding clusters' labels Added new internal function niceFactorLevels() that ensures all the factors' levels will have labels with the same length, via padding the integers values with '0' and string values with '_' Relaxed tolerance on tests comparing against saved data Changes in version 2.1.4 Speed-up by use of parallelDist::parDist() to calculate distances instead of stats::dist() Fixed regression tests failing on non-Linux architectures Changes in version 2.1.3 Completed function clustersMarkersHeatmapPlot() Added new utility function normalizeNameAndLabels() Added mergeClusters() and multiMergeClusters() functions Added support to conditions in cells' meta-data Now clusterizations are stored as factors Fixed COTAN::validity method in AllClasses.R Changes in version 2.1.2 Fixed bug in proceedToCoex() in cases when saveObj == TRUE Changes in version 2.1.1 Updated README.md and NEWS.md Renamed methods dealing with housekeeping genes and fully-expressed cells to use the more proper names fully-expressed genes and fully-expressing cells Added possibility to users to set the cutoff and thresholds used by the clean and related methods Changes in version 2.1.0 First release in Bioconductor 3.18 Changes in version 1.99.4 Solved remaining documentation warnings Changes in version 1.99.3 Updated the vignette, README.md and NEWS.md Changes in version 1.99.2 Dropped second vignette: will be merged in the other one... Changes in version 1.99.1 Minor bug fixes and new function clustersMarkersHeatmapPlot() Changes in version 1.99.0 Included new functionalities for Bioc 2.17 release: - created a new COTAN class to replace the old scCOTAN: this class provides internal invariants along a wide host of accessors that allows users to avoid peeking inside the class - made a new multi-core implementation of the model parameters estimations and COEX calculations that achieves much higher speeds. - added new functionality about gene clusters starting from given markers lists - added new functionality about uniform cell clustering based on the maximum GDI level in the cluster - added function to get a differential expression estimation for each cluster against background - added function to get an enrichment score for each cluster given a list of markers specific for the cells' population - added plots to asses data-set information at cleaning stage Changes in version 0.99.13 After official release. PCA function changed to avoid basilisk and Python. Changes in version 0.99.12 Release before the official release of Bioc 3.15. Main changes: - The way in which the COEX matrix is estimated and stored is changed to occupy less space and run faster. Changes in version 0.99.10 Initial Bioconductor release