Changes in version 2.6.1 Improved function clustersMarkersHeatmapPlot(): now its shows a column for each marker gene and the shown content is more expressive Marked the function clustersDeltaExpression() as legacy: it has been replaced with the function DEAOnClusters() in the package Fixed minor bug in class AdvancedGDIUniformityCheck regarding third check: was testing third highest GDI value instead of second Changes in version 2.5.11 Fixed bug in the function cellsUMAPPlot(): restored possibility of passing a genes vector as genesSel parameter. Also updated the documentation about the available genes selection methods Changes in version 2.5.10 Fixed typo in error message Fixed bug in function genesCoexSpace(): now primaryMarkers can have only a single gene Changes in version 2.5.9 Exported utility functions about names arrays: conditionsFromNames(), niceFactorLevels(), factorToVector() Changes in version 2.5.8 feature/add_condition_arguments_to_plot_functions Now the following plot functions take in conditions explicitly, instead of just instructions to determine them from the cells' names. The changes involved: cellSizePlot(), ECDPlot(), genesSizePlot(), mitochondrialPercentagePlot(), scatterPlot() Added possibility to convert COTAN objects to/from SingleCellExperiment objects. SCE objects created by the Seurat package are supported Hardened arguments' checks for function UMAPPlot() Solved issue with the function establishGenesClusters(): it was throwing an error when one of the sub-lists in the groupMarkers argument did contain only one element Changes in version 2.5.7 Introduced new way to check for the Uniform-Transcript property of the clusters based on multiple thresholds calibrated so that the new method is more effective at describing really statistically uniform clusters Functions cellsUniformClustering() and mergeUniformCellsClusters() have been re-factored so to support new class hierarchy for UT checkers. This allows user to select which method to use for the checks; as of now the following methods are supported: - "SimpleGDIUniformityCheck" - "AdvancedGDIUniformityCheck" Avoided issue with pdf file creation: file handle was not closed in case of errors Added possibility of choosing number of features in seuratHVG() Solved minor issue with with clusterization functions in cases when only one cluster was created Changes in version 2.5.6 Made function heatmapPlot() more easy to use and in line with the rest of the COTAN package Now the method storeGDI() can take in the output data.frame from the function calculateGDI() Solved few minor issues with the vignette and changed a few default parameters in cellsUMAPPlot(), pValueFromDEA() and findClustersMarkers() Changes in version 2.5.5 Stopped function cellsUniformClustering() from saving the internally created Seurat object due to possibly long saving times Split the now deprecated function getNormalizedData() into two separated functions: getNuNormData() and getLogNormData() Re-factored function mergeUniformCellsClusters() to be more precise: now it merges clusters starting from the most similar in latest batch and also runs the merging in multiple steps adjusting gradually the GDI threshold ranging from a very strict up to the user given ones. Fixed minor bugs in functions GDIPlot() and clustersMarkersHeatmapPlot() Changes in version 2.5.4 Added possibility to display UMAP plots of cells clusters, using the function cellsUMAPPlot() Changes in version 2.5.3 Updated the vignette to the most recent changes Allowed user to set the ratio of genes above the threshold allowed in a Uniform Transcript cluster Changes in version 2.5.2 Solved issue with usage checks about the torch library Allowed user to explicitly opt-out from the torch library usage: COTAN will avoid torch commands when the option "COTAN.UseTorch" is set to FALSE Changes in version 2.5.1 Added support for the torch library to help with the heavy lifting calculations of the genes' COEX matrix, with consequent substantial speed-up, especially when a GPU is available on the system Changes in version 2.5.0 First release in Bioconductor 3.20 Changes in version 2.3.6 Refactored DEAOnCluster() to make it run faster. Now clustering functions dump the GDI check results for all clusters Changed default GDI threshold to 1.43 Added new input to mergeUniformCellsClusters() to allow proper resume of interrupted merges Added possibility to query whether the COEX matrix is available in a COTAN object Changes in version 2.3.5 Made checks more strict when adding a clusterization or condition Increased reliability of clustering functions by improved error handling and by allowing retry runs on estimators functions Changes in version 2.3.4 Speed-up of GDI calculation via Rfast package Added possibility of using distance between clusters based on Zero-One matrix instead of DEA Added average floor to logFoldChangeOnClusters() to dampen extreme results when genes are essentially absent from a cluster. Changes in version 2.3.3 Added method to handle expression levels' change via log-normalized data: logFoldChangeOnClusters() Minor fix in the import of operators to align to new version of roxigen2 Restored default adjustment method of pValueFromDEA() to "none" for backward compatibility reasons Changes in version 2.3.2 Solved issue with cleanPlots() when the number of cells exceeded 65536 Added methods to calculate the COEX matrix only on a subset of the columns Now the function pValueFromDEA() returns the p-value adjusted for multi-test Changes in version 2.3.1 Stopped using explicit PCA via irlba package: using BioConductor PCAtools::pca instead Changes in version 2.3.0 First release in Bioconductor 3.19 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