- 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 usersâ€™ 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.