NEWS

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dominoSignal 0.99.4

Vignettes

• Updated download instructions to use the bioconductor URL

dominoSignal 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

dominoSignal 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

dominoSignal 0.99.1

• Update to Bioconductor version numbering conventions for package submission

dominoSignal 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

dominoSignal 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