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