• The package vignettes are updated.

  • The betweenness function is corrected.

  • Documentation of some functions corrected.

  • Links to my personal website are corrected.

  • The package vignettes are updated.

  • The implementations of shiny apps are optimized.

  • Shiny apps are debugged.

  • A new argument, label.position, is added to the exir.vis function.

  • The exir.vis function is debugged and optimized.

  • The upload file size limit is removed from the local shiny apps.

  • The package website built with pkgdown is added to github.

  • The default correlation coefficient is changed from 0.3 to 0.5 in the ExIR function and its shiny app.

  • The ExIR shiny app is debugged and updated.

  • The ExIR function is debugged and updated.

  • The DESCRIPTION file is updated.

  • The function ExIR as well as the ExIR shiny app are debugged.

  • Documentations of some functions are updated.

  • The DESCRIPTION file is updated.

  • The name of the function for running shiny apps is changed to runShinyApp.

  • Shiny apps are updated in the package for local use.

  • Documentations of several functions are updated.

  • The Vignettes are updated.

  • The Read Me file is updated.

  • Update package Vignettes.

  • Documentation on how to access ExIR shiny app is added to the Read Me file, vignettes, and the corresponding functions’ documentations.

  • The ExIR shiny app is added to the package.

  • A Shiny app is developed for the running the ExIR model and visualization of its output.

  • Add the comp_manipulate function for the simulation of gene knockout and up-regulation.

  • Debug the function IVI.

  • Debug the function ExIR.

  • Add dependence to R package janitor for the correction of illegal characters in feature names.

  • Documentation on how to access IVI shiny app is added to the Read Me file, vignettes, and the corresponding functions’ documentations.

  • The IVI shiny app is added to the package.

  • A Shiny app is developed for the calculation of IVI as well as IVI-based network visualization.

  • The dependence of the function ExIR on the package reshape2 is removed.

  • The function ExIR is debugged.

  • The function ExIR is debugged.
  • The ReadMe file is updated.

  • The citation details of the package is updated.

  • Vignettes of the package are updated and extended.

  • A new function named exir.vis is added for the visualization of the results of the function exir.

  • A new function named cent_network.vis is added for the visualization of a network based on a centrality measure.

  • A new function named graph_from_incidence_matrix is added (imported from the igraph package) for the network reconstruction from an incidence matrix.

  • A new column named Type is added to the Biomarker table of the function ExIR.

  • The Z-score and statistical significance are added to the results of the function ExIR.

  • The function ExIR is updated so that the experimental data are ranked prior to correlation analysis. This will result in the assessment of the association based on the Spearman method, a more robust algorithm in variable conditions and/or non-parametric distributions.

  • The version of Roxygen2 is updated in the DESCRIPTION file.

  • The documentation of the ExIR function is updated.

  • The ExIR function is updated to prevent outputting NULL results.

  • The package logo is updated in accordance with the logo design of well-known R packages.

  • Some documentations in the Read Me file are corrected.

  • The NC function is improved.

  • The documentation of the exir function is updated.

  • The DESCRIPTION file is updated according to all of the modifications.

  • The citation details of the package is updated.

  • The function diff.data.assembly is added for assembling the differential/regression data required as an input for the exir function.

  • The function exir is added for the experimental-data-based classification and ranking of top candidate features.

  • The function clusterrank is upgraded to clusterRank in order to calculate the ClusterRank centrality internally.

  • The function neighborhood.connectivity is undergone minor modifications to enhance the performance speed.

  • The function sif2igraph is added for automatic importing and conversion of a SIF file from the users’ local hard drive, cloud space, or internet into a graph with an igraph class.

  • The thesis advisors are added to the DESCRIPTION file.

  • Some minor corrections are done in the documentation of functions and DESCRIPTION file.

  • The DESCRIPTION file is updated.

  • The Vignettes file is updated.

  • The function sirir is added for the unsupervised influence ranking of network nodes.

  • The function hubness.score is added for the calculation of the Hubness score.

  • The function spreading.score is added for the calculation of the Spreading score.

  • The function ivi is added for the influential node identification from a graph.

  • The function ivi.from.indices is added for the influential node identification from indices.

  • The function ihs is removed as a refined formula is added for influential node identification.

  • Updating the normality assessment results of association functions for vectors of length < 4

  • The function clusterrank is added for the calculation of ClusterRank.

  • The function collective.influence is added for the calculation of Collective Influence.

  • The function lh_index is added for the calculation of local H-index.

  • The function h_index is added for the calculation of H-index.

  • The function neighborhood.connectivity is updated so that it will not return any NA or NaN values and the output will be a numeric vector.

  • The formatting of return values in the documentation of each function is corrected.

  • The citation details of the package are updated according to its associated published paper.

  • The error regarding the use of NNS since the second use of association assessment functions including cond.prob.analysis and double.cent.assess.noRegression is now corrected.