Performance Benchmarking of the R Programming Environment on the Stampede 1.5 Supercomputer

Author(s):  
James R. McCombs ◽  
Scott Michael
F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1774 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Shraddha Pai ◽  
Ruth Isserlin ◽  
Barry Demchak ◽  
Alexander R. Pico

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.


F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1774 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Shraddha Pai ◽  
Ruth Isserlin ◽  
Barry Demchak ◽  
Alexander R. Pico

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.


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

2019 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Shraddha Pai ◽  
Ruth Isserlin ◽  
Barry Demchak ◽  
Alexander R. Pico

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.


2021 ◽  
pp. 155-179
Author(s):  
Vinay Babu ◽  
J. Devaraju

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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