# CatsCradle 

<img src="CatsCradleLogoTransparent.png" alt="" width="200"/>

CHANGES IN VERSION 0.99.10
--------------------------

* We have now broken out our code into files pertaining to different
  areas of functionality.
* We have improved functionality for
  handling SingleCellExperiment and SpatialExperiment objects.
* CatsCradle is currently under review at Bioconductor.  Watch this
  space.

CHANGES IN VERSION 1.1.1
--------------------------

* Default behaviour of nbhdsAsEdgesToNbhdsAsList changed to exclude 
  self. This fixes a bug leading to inflated values of MoransI.
  
CHANGES IN VERSION 1.1.2
--------------------------

* Function getSubsetComponents added. This is designed to dectect the 
  components of a gene subset in the case where median complement distance
  detects clustering.
* Function edgeLengthsAndCellTypePairs rewritten for faster runtime.

CHANGES IN VERSION 1.3.1
--------------------------

* smallXenium@images$fov@misc = list() field added to smallXenium example
  data for compatability with Seurat updates.
  
CHANGES IN VERSION 1.3.2
--------------------------

* Function getLigandReceptorPairsInPanel rewritten for faster runtime.
* Analytical option to calculate pvalues added to computeNeighbourEnrichment.
  This has a faster runtime.
* Function performLigandReceptorAnalysis rewritten for faster runtime by 
  making use of sparse matrices.
* Analytical option to calculate pvalues added to  performLigandReceptorAnalysis.
  This has a faster runtime.
* Function plotLRDotplot added to visualise ligand-receptor interactions returned
  by performLigandReceptorAnalysis.
  
CHANGES IN VERSION 1.3.3
--------------------------

* Example data ligandReceptorResults.rda saved in compressed format.

CHANGES IN VERSION 1.7.1
--------------------------

* Bugfix to allow use of user-provided LRN.
* Remove check that species is human or mouse if LRN is provided by user.
* Heirachical ordering of LRInteraction heatmap.
