Changelog

Source: NEWS.md

ChromSCape 1.1.3

Major Changes

* Support "multi-feature" analysis, e.g. parallel analysis of multiple 
features (bins, peaks or gene) on the same object.

* New "Coverage" tab & functions generate_coverage_tracks() and
plot_coverage_BigWig() to generate cluster coverage tracks and interactively 
visualise loci/genes of interest in the application.

* New inter- and intra-correlation violin plots to vizualise cell correlation
distribution between and within clusters.

* New normalization method : TF-IDF combined with systematic removal of PC1
strongly correlated with library size.

* Simple 'Copy Number Alteration' approximation & visualization using 
'calculate_CNA' function for genetically re-arranged samples, provided one 
or more control samples.

* New generate_analysis() & generate_report() functions to run a full-on 
ChromSCape analysis and/or generate an HTML interactive report of an existing analysis.

* Supports 'custom' differential analysis to find differential loci between
a subset of samples and/or clusters.

* New pathway overlay on UMAP to visualize cumulative pathways signal 
directly on cells.

* Now supports 'Fragment Files' input (e.g. from 10X cell ranger scATAC
pipeline), using a wrapper around 'Signac' package FeatureMatrix() function.

* New 'Contribution to PCA' plots showing most contributing features and 
chromosome to PCA.

* Restructuration of the ChromSCape directory & faster reading/saving of 
S4 objects using package 'qs'.

Minor Changes

* RAM optimisation & faster pearson cell-to-cell correlations with 'coop'
package, and use of 'Rcpp' for as_dist() RAM-efficient distance calculation.

* Faster correlation filtering using multi-parallel processing.

* plot_reduced_dim now supports gene input to color cells by gene signal.

* All plots can now be saved in High Quality PDF files.

* Changed 'geneTSS' to 'genebody' with promoter extension to better reflect
the fact that mark spread in genebodies.

* Possibility to rename samples in the application.

* Downsampling of UMAPs & Heatmaps for fluider navigation.

* Changed 'total cell percent based' feature selection to manual selection of
top-covered features, as the previous was srongly dependent on the experiment size.

* Faster sparse SVD calculation.

* Faster differential analysis using pairWise Wilcoxon rank test from 'scran'
package.