Package: ceRNAnetsim 1.17.0

Selcen Ari Yuka

ceRNAnetsim: Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables.

Authors:Selcen Ari Yuka [aut, cre], Alper Yilmaz [aut]

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ceRNAnetsim.pdf |ceRNAnetsim.html✨
ceRNAnetsim/json (API)
NEWS

# Install 'ceRNAnetsim' in R:
install.packages('ceRNAnetsim', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/selcenari/cernanetsim/issues

Datasets:

On BioConductor:ceRNAnetsim-1.17.0(bioc 3.20)ceRNAnetsim-1.16.0(bioc 3.19)

bioconductor-package

12 exports 0.91 score 60 dependencies 1 mentions

Last updated 2 months agofrom:e399d6eb46

Exports:calc_perturbationfind_affected_nodesfind_iterationfind_node_perturbationfind_targeting_nodespriming_graphsimulatesimulate_visupdate_howupdate_nodesupdate_variablesvis_graph

Dependencies:cachemclicodetoolscolorspacecpp11digestdplyrfansifarverfastmapfurrrfuturegenericsggforceggplot2ggraphggrepelglobalsgluegraphlayoutsgridExtragtableigraphisobandlabelinglatticelifecyclelistenvmagrittrMASSMatrixmemoisemgcvmunsellnlmeparallellypillarpkgconfigpolyclippurrrR6RColorBrewerRcppRcppArmadilloRcppEigenrlangscalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewithr

Calculating Number of Iterations Required to Reach Steady-State

Selcen Ari

Rendered fromconvenient_iteration.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2019-11-25
Started: 2019-03-15

A TCGA dataset application

Selcen Ari

Rendered frommirtarbase_example.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2019-11-26
Started: 2019-03-18

The auxiliary commands which can help to the users

Selcen Ari

Rendered fromauxiliary_commands.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2019-11-26
Started: 2019-08-06

Basic Use of ceRNAnetsim

Selcen Ari

Rendered frombasic_usage.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2019-11-24
Started: 2019-08-06

Readme and manuals

Help Manual

Help pageTopics
Calculates average expression changes of all nodes except trigger and finds the perturbed node count for a given node.calc_perturbation
Finds top affected nodes for perturbation from a particular nodefind_affected_nodes
Finds the iteration which provides maximum affected node numberfind_iteration
Calculates average expression changes of all (or specified) nodes except trigger and finds the perturbed node count for all (or specified) nodes in system.find_node_perturbation
Finds potential affecting node for given particular target.find_targeting_nodes
huge examplehuge_example
midsampmidsamp
midsamp_new_countsmidsamp_new_counts
minsampminsamp
mirtarbasegenemirtarbasegene
new_countsnew_counts
Converts the given dataframe using first variable as competing and the second as miRNA. The function converts the given dataframe using first variable as competing and the second as miRNA. If user defines interaction factors as affinity or degradation, the factors are taken into account.priming_graph
Utilizes the change in expression value/s as triggering.simulate
Provides visualisation of the graph in addition to simulate function.simulate_vis
TCGA_E9_A1N5_mirnanormalTCGA_E9_A1N5_mirnanormal
TCGA_E9_A1N5_mirnatumorTCGA_E9_A1N5_mirnatumor
TCGA_E9_A1N5_normalTCGA_E9_A1N5_normal
TCGA_E9_A1N5_tumorTCGA_E9_A1N5_tumor
Converts the count value of the given node.update_how
Carries variables from edge to node.update_nodes
Replaces new values with previous values of competing or miRNA counts.update_variables
Provides visualisation of the graph.vis_graph