NEWS.md

In seriph78/COTAN: COexpression Tables ANalysis

2.5.2

Solved issue with usage of 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

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

COTAN 2.5.0

First release in Bioconductor 3.20

COTAN 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

COTAN 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

COTAN 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.

COTAN 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

COTAN 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

COTAN 2.3.1

Stopped using explicit PCA via irlba package: using BioConductor PCAtools::pca instead

COTAN 2.3.0

First release in Bioconductor 3.19

COTAN 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

COTAN 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

COTAN 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

COTAN 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

COTAN 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

COTAN 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

COTAN 2.1.2

Fixed bug in proceedToCoex() in cases when saveObj == TRUE

COTAN 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

COTAN 2.1.0

First release in Bioconductor 3.18

COTAN 1.99.4

Solved remaining documentation warnings

COTAN 1.99.3

Updated the vignette, README.md and NEWS.md

COTAN 1.99.2

Dropped second vignette: will be merged in the other one...

COTAN 1.99.1

Minor bug fixes and new function clustersMarkersHeatmapPlot()

COTAN 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

COTAN 0.99.13

After official release. PCA function changed to avoid basilisk and Python.

COTAN 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.

COTAN 0.99.10

Initial Bioconductor release

seriph78/COTAN documentation built on May 17, 2024, 5:34 a.m.