Changes in version 2.4.6                        

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 2.4.5                        

Avoided issue with pdf file creation: file handle was not closed in case
of errors

Solved minor issue with with clusterization functions in cases when only
one cluster was created

                        Changes in version 2.4.4                        

Made function heatmapPlot() more easy to use and in line with the rest
of the COTAN package

Solved few minor issues with the vignette and changed a few default
parameters in pValueFromDEA() and findClustersMarkers()

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()

Fixed minor bugs in function clustersMarkersHeatmapPlot()

                        Changes in version 2.4.3                        

Updated vignette to the most recent changes

                        Changes in version 2.4.2                        

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

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 2.4.1                        

Fixed bug in reorderClusterization() function

                        Changes in version 2.4.0                        

First release in production

                        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