R-CHIE statistics

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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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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 in pipeline

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

[…] 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 […]


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R-CHIE in publications

 (11)
PMCID: 5886760
PMID: 29409859
DOI: 10.1016/j.molp.2018.01.008

[…] 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 ()., it is well known that cds gc content is bimodal (, , ), so we fitted a one-dimensional gaussian mixture model with two components […]

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

[…] 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 […]

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

[…] 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 […]

PMCID: 5499600
PMID: 28449096
DOI: 10.1093/nar/gkx303

[…] 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., the stoichiometry of 40s […]

PMCID: 5330540
PMID: 28192430
DOI: 10.1371/journal.pcbi.1005383

[…] sec-containing lineage in archaea, includes a trnasec with a 7 bp d-stem and an intron in the t arm []., 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 […]


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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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