R-CHIE statistics

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Citations per year

Number of citations per year for the bioinformatics software tool R-CHIE
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Tool usage distribution map

This map represents all the scientific publications referring to R-CHIE per scientific context
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R-CHIE specifications

Information


Unique identifier OMICS_09289
Name R-CHIE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Irmtraud M. Meyer

Information


Unique identifier OMICS_09289
Name R-CHIE
Interface Web user interface
Restrictions to use None
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Irmtraud M. Meyer

Publication for R-CHIE

R-CHIE citations

 (12)
library_books

Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants

2018
Mol Plant
PMCID: 5886760
PMID: 29409859
DOI: 10.1016/j.molp.2018.01.008

[…] PPV and sensitivity calculation. The F1 score was calculated from the previous definition (). When comparing PPV in CDS between rice and Arabidopsis, mRNAs were filtered by length as described above. R-CHIE was used for visualizing the folded RNAs (). […]

library_books

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

2018
Front Microbiol
PMCID: 5758548
PMID: 29354101
DOI: 10.3389/fmicb.2017.02582

[…] ier to interpret (e.g., Figures , respectively). These diagrams can be generated using VARNA, which requires dot-bracket notation as the input (Darty et al., ). Arc diagrams can also be created using R-CHIE, which is available as R package and web service (Lai et al., ).However, these diagrams and dot-bracket notation normally represent one sequence at a time. Often common RNA elements are found i […]

library_books

RNA editing by ADAR1 leads to context dependent transcriptome wide changes in RNA secondary structure

2017
Nat Commun
PMCID: 5682290
PMID: 29129909
DOI: 10.1038/s41467-017-01458-8

[…] 00 reads with editing level G/(A + G) > 0.1 on average in the control samples, were changed from A-to-G prior to modeling.Visualization of 2D RNA structures were done using RNAplot of Vienna package. R-chie was used to draw the arc diagrams of the RNA 2D structures (as in Fig. ).In order to compare structural ensembles in control and KD samples, we used RNAsubopt of Vienna package with 1000 random […]

library_books

Numerical integration methods and layout improvements in the context of dynamic RNA visualization

2017
BMC Bioinformatics
PMCID: 5450055
PMID: 28558664
DOI: 10.1186/s12859-017-1682-0

[…] reviews of them can be found in [, ], with notable examples that are still available including VARNA [], jViz.RNA [–], Forna [], PseudoViewer [–], 4SALE [, ], Assemble2 [, ], RNA2DMap [], R2R [], and R-Chie []. All Visualization software developed for RNA have as their goal to display an informative structure of the RNA molecule, usually focusing on its secondary structure, that can be annotated a […]

library_books

Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame

2017
Nucleic Acids Res
PMCID: 5499600
PMID: 28449096
DOI: 10.1093/nar/gkx303

[…] ucture turned out to be quite robust, and was impervious to the choice of alternative thresholds (0.4–0.7), or reagent type (NMIA). Finally, the selected structure was evaluated for covariation using R-Chie () and 67 sequences from the ‘los Alamos compendium’ representing the variability of HIV-1 (see ), the results were used as a basis for a marginal manual refinement. […]

library_books

Computational identification of the selenocysteine tRNA (tRNASec) in genomes

2017
PLoS Comput Biol
PMCID: 5330540
PMID: 28192430
DOI: 10.1371/journal.pcbi.1005383

[…] We evaluated the conservation of the tRNASec structure across eukaryotes. We used the program R-chie [] to analyze the structural alignment containing the top scoring predictions in the benchmark set. The alignment largely supports the eukaryotic tRNASec structural model [, ], showing covariat […]


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R-CHIE institution(s)
Department of Computer Science; Department of Medical Genetics, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada

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