Releases: asalavaty/influential
v2.2.7 is released on CRAN Latest
The README file is updated.
DESCRIPTION of the package is updated.
New packages including foreach, and doParallel are added to the Imports section of the DESCRIPTION.
ExIR function, exir, is optimized by providing access to several cores. Also, its documentation is updated.
IVI function, IVI, is optimized by providing access to several cores. Also, its documentation is updated.
LH-index function, clusterRank, is optimized by providing access to several cores. This also significantly speeds up the ivi function. Also, its documentation is updated.
LH-index function, lh_index, is optimized by providing access to several cores. This also significantly speeds up the ivi function. Also, its documentation is updated.
A verbose argument is added all centrality measure functions and their corresponding documentations are updated as well.
The fcor function, fcor, as well as its documentation are optimized and updated.
The documentation of the SIRIR function, sirir, is updated.
Hubness score function, hubness.score, is debugged and optimized.
Spreading score function and its documentation, spreading.score, is debugged and optimized.
IVI function, ivi, is debugged and optimized.
IVI from indices function, ivi.from.indices, is debugged and optimized.
Collective Influence function, collective.influence, is optimized.
The documentation of the Collective Influence function, collective.influence, is updated.
v2.2.6 is released on CRAN
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.
v2.2.5 is released on CRAN
Update the ExIR function.
v2.2.4 is released on CRAN
Update the ExIR vis figure.
v2.2.3 is released on CRAN
The ExIR shiny app is debugged and updated.
The ExIR function is debugged and updated.
v2.2.2 is released on CRAN
The DESCRIPTION file is updated.
The function ExIR, as well as the ExIR shiny app, are debugged.
Documentations of some functions are updated.
v2.2.1 is released on CRAN
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.
v2.2.0 is released on CRAN
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.
v2.0.0 released on CRAN
The ReadMe file is updated.
The citation details of the package are 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 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 design of R packages.
Some documentations in the Read Me file are corrected.
v1.1.2 released on CRAN
The NC function is improved.
The documentation of the exir function is updated.