ExIR Shiny app is updated according to the ExIR function.
ExIR visualization function, exir.vis
, is optimized.
The package vignettes are updated and the fcor
function described
and exemplified in the vignettes.
The ExIR function is optimized (corrected for proper Spearman correlation analysis and added Mutual rank as a measure for filtering top correlations) and speeded up (using the data.table package).
A function named fcor
is added to the package for super-fast
correlation analysis of large datasets and simultaneous P-value and
Mutual Rank calculations.
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 functionsâ€™ 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 functionsâ€™ 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.
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.
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