Changes in version 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.