Overview of the R Programming Environment, Installations, and Basic Syntax

2018 ◽  
pp. 1-7
Author(s):  
Khameel Bayo Mustapha
Keyword(s):  
Programming Environment ◽  
R Programming

scholarly journals RCy3: Network biology using Cytoscape from within R

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1774 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Shraddha Pai ◽  
Ruth Isserlin ◽  
Barry Demchak ◽  
Alexander R. Pico
Keyword(s):  
Shortest Path ◽  
Future Development ◽  
Enrichment Analysis ◽  
Network Biology ◽  
R Package ◽  
Programming Environment ◽  
R Packages ◽  
R Programming ◽  
Shortest Path Algorithms ◽  
Rest Api

RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort. Over 100 new functions have been added, including dozens of helper functions specifically for intuitive data overlay operations. Over 40 Cytoscape apps have implemented automation support so far, making hundreds of additional operations accessible via RCy3. Two-way conversion with networks from \textit{igraph} and \textit{graph} ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages. These capabilities are demonstrated in a series of use cases involving public databases, enrichment analysis pipelines, shortest path algorithms and more. With RCy3, bioinformaticians will be able to quickly deliver reproducible network biology workflows as integrations of Cytoscape functions, complex custom analyses and other R packages.

scholarly journals RCy3: Network biology using Cytoscape from within R

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1774 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Shraddha Pai ◽  
Ruth Isserlin ◽  
Barry Demchak ◽  
Alexander R. Pico
Keyword(s):  
Shortest Path ◽  
Future Development ◽  
Enrichment Analysis ◽  
Network Biology ◽  
R Package ◽  
Programming Environment ◽  
R Packages ◽  
R Programming ◽  
Shortest Path Algorithms ◽  
Rest Api

RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort. Over 100 new functions have been added, including dozens of helper functions specifically for intuitive data overlay operations. Over 40 Cytoscape apps have implemented automation support so far, making hundreds of additional operations accessible via RCy3. Two-way conversion with networks from \textit{igraph} and \textit{graph} ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages. These capabilities are demonstrated in a series of use cases involving public databases, enrichment analysis pipelines, shortest path algorithms and more. With RCy3, bioinformaticians will be able to quickly deliver reproducible network biology workflows as integrations of Cytoscape functions, complex custom analyses and other R packages.

scholarly journals Fault tree analysis in the R programming environment

Dependability ◽  
2018 ◽  
Vol 18 (1) ◽  
pp. 4-13 ◽  
Author(s):  
Alexander V. Antonov ◽  
Evgeny Yu. Galivets ◽  
Valery A. Chepurko ◽  
Alexey N. Cherniaev
Keyword(s):  
Fault Tree ◽  
Fault Tree Analysis ◽  
Programming Environment ◽  
Tree Analysis ◽  
R Programming

scholarly journals RCy3: Network Biology using Cytoscape from within R

2019 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Shraddha Pai ◽  
Ruth Isserlin ◽  
Barry Demchak ◽  
Alexander R. Pico
Keyword(s):  
Shortest Path ◽  
Future Development ◽  
Enrichment Analysis ◽  
Network Biology ◽  
R Package ◽  
Programming Environment ◽  
R Packages ◽  
R Programming ◽  
Shortest Path Algorithms ◽  
Rest Api

AbstractRCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort. Over 100 new functions have been added, including dozens of helper functions specifically for intuitive data overlay operations. Over 40 Cytoscape apps have implemented automation support so far, making hundreds of additional operations accessible via RCy3. Two-way conversion with networks from igraph and graph ensures interoperability with existing network biology workflows and dozens of other Bioconductor packages. These capabilities are demonstrated in a series of use cases involving public databases, enrichment analysis pipelines, shortest path algorithms and more. With RCy3, bioinformaticians will be able to quickly deliver reproducible network biology workflows as integrations of Cytoscape functions, complex custom analyses and other R packages.

Evaluating chemical weathering of sediments using “R” programming environment – A possible alternate of spreadsheet applications

2021 ◽  
pp. 155-179
Author(s):  
Vinay Babu ◽  
J. Devaraju
Keyword(s):  
Chemical Weathering ◽  
Correlation Coefficients ◽  
Foreland Basin ◽  
Skewed Distribution ◽  
Compositional Variation ◽  
Programming Environment ◽  
User Requirement ◽  
Elemental Geochemistry ◽  
Statistical Measures ◽  
R Programming

Evaluation of chemical weathering of sediments is the key factor for provenance study and characterization of various sedimentological processes involved in weathering. The various Weathering Indices (WIs) models are available to estimate major elemental geochemistry of the sedimentary package including CIW, CPA, CIA, PIA, CIX, ICV, WIP, R, V, STI and MWPI. The present investigation is to improve and correlation of the earlier models with our development of a computer program using R programming environment to establish various statistical measures, correlation of chemical indices of weathering and to plot different compositional variation diagrams and their analyses. The present results reveal that the correlation of Different correlation plots suggest a significant level of relationship and positive correlation coefficients in CIW – PIA, CIA – PIA, CPA – CIX, ICV – MWPI pairs while significant level of relationship and negative correlation coefficients in CIW – ICV, CIA – WIP pairs. Besides, boxplot of WIs indicates a skewed left or negatively-skewed distribution of CIW and CIA while a skewed right or positively-skewed distribution of CPA, CIX and WIP. Different compositional space diagrams (A – C – N, A – CN – K, A-K – C – N, M – F – W, A – CNK – FM, A – N – K) constrain sediments and rock/mineral composites major elemental geochemistry and demonstrate weathering profiles and source rock chemical makeup. R environment provides flexibility to alter the code as per the data and user requirement by altering different arguments in the code and to include further relevant charts & plots. The applicability of the programming tool is demonstrated by its performance in evaluating the chemical weathering of Surma and Barail sandstones, Mizoram Foreland Basin, NE India and sediments of Manasbal Lake, Kashmir, India, having contrasting provenance histories.

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