Changes in version 0.99.4                        

Vignettes

  - Updated download instructions to use the bioconductor URL

                       Changes in version 0.99.3                        

create_domino Function Warnings

  - Disabled exact p-value computation for the correlation test between
    receptor expression and features to prevent repeated warning
    messages due to tied ranks during Spearman correlation calculation

Vignettes

  - Updated non-functional links to functional URLs
  - All vignettes explicitly state the seed used when executing their
    code
  - The dominoSignal Object vignette states the purpose of the code used
    to download and import data from a BioFileCache to demonstrate
    applications of the domino objects on a real data object that is too
    large to include inside the package

Testing Data

  - Data used for examples and unit tests is now stored in the package's
    data/ directory.
  - All usage of the triple colon operator to access internal data from
    sysdata have been replaced with usage of data()
  - Linkage summaries for demonstrating differential linkage testing and
    plotting are generated within unit test scripts rather than being
    stored within the package.
  - Examples are run with echo = FALSE to cut down on lines of code
    printed in example pages.
  - Examples for create_domino are run with verbose = FALSE
  - Fixed example of changing colors for circos_ligand_receptor
  - Fixed example of boolean representation of cor_heatmap

                       Changes in version 0.99.2                        

Package Name

  - Update of package name from "domino2" to "dominoSignal"

Bioconductor Standards

  - Update to vignettes presenting application of the DominoSignal
    pipeline on data formatted as a SingleCellExperiment object
  - Implemented caching of example data by BiocCache to meet package
    size limits
  - Removal of deprecated scripts for running SCENIC. Tutorials for
    running SCENIC are still present in vignettes
  - Corrected BiocCheck notes pertaining to coding practices including
    paste in conditional statements, functions with dontrun examples,
    usage of seq_len or seq_along in place of seq, and usage of vapply
    in place of sapply

                       Changes in version 0.99.1                        

  - Update to Bioconductor version numbering conventions for package
    submission

                        Changes in version 0.2.2                        

Linkage functions

  - Addition of new class to summarize linkages in objects
  - Addition of helper functions to count linkages and compare between
    objects
  - Plotting function for differential linkages

Package structure

  - Adjustments made to meet Bioconductor standards

                        Changes in version 0.2.1                        

Updates to domino object construction

  - Uniform formats for inputs of receptor - ligand interaction
    databases, transcription factor activity features, and regulon gene
    lists for operability with alternative databases and transcription
    factor activation inference methods
  - Helper functions for reformatting pySCENIC outputs and CellPhoneDB
    database files to domino-readable uniform formats
  - Assessment of transcription factor linkage with receptors that
    function as a heteromeric complex based on correlation between
    transcription factor activity and all receptor component genes
  - Assessment of complex ligand expression as the mean of component
    gene expression for plotting functions
  - Minimum threshold for the percentage of cells in a cluster
    expressing a receptor gene for the receptor to be called active
    within the cluster
  - Additional linkage slots for active receptors in each cluster,
    transcription factor - receptor linkages for each cluster, and
    incoming ligands for active receptors on each cluster

Plotting functions

  - Chord plot of ligand expression targeting a specified receptor where
    chord widths correspond to the quantity of ligand expression by each
    cell cluster
  - Signaling networks showing only outgoing signaling from specified
    cell clusters
  - Gene networks between two cell clusters

Bugfixes

  - Added host option for gene ortholog conversions using {biomaRt} for
    access to maintained mirrors
  - Transcription factor - target linkages are now properly stored so
    that receptors in a transcription factor's regulon are excluded from
    linkage
  - Ligand nodes sizes in gene networks correspond to quantity of ligand
    expression
  - create_domino() can be run without providing a regulon list
  - References to the host GitHub repository have been updated to
    Elisseeff-Lab