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CanDrA specifications

Information


Unique identifier OMICS_05373
Name CanDrA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Ken Chen

Publication for CanDrA

CanDrA citations

 (3)
library_books

Next generation mapping reveals novel large genomic rearrangements in prostate cancer

2017
Oncotarget
PMCID: 5410329
PMID: 28423598
DOI: 10.18632/oncotarget.15802

[…] nucleotide variants; del, deletion; ins, insertion; dup, duplication; inv, inversion., ausing functional prediction tools gemini, sift and polyphen2., bdriver mutation prediction using transfic and candra identified a single mutation by both methods within atrx gene., cdefined as ‘high’ impact by the gemini sequence ontology., dinspection of genecards and pubmed identified the following genes […]

library_books

Notch pathway activation is essential for maintenance of stem like cells in early tongue cancer

2016
Oncotarget
PMCID: 5226594
PMID: 27391340
DOI: 10.18632/oncotarget.10419

[…] analysis for somatic non-synonymous variants using nine different tools such as: dbnsfp v2.0 (includes sift, polyphen2_hdiv, polyphen2_hvar, lrt, mutation taster, mutation accessor and fathmm) [], candra v1.0 [] and provean v.1.1 []. variants called deleterious in nature by at least one software was taken for further analysis. we confirmed the identity of mutations by manual visualization […]

library_books

Benchmarking mutation effect prediction algorithms using functionally validated cancer related missense mutations

2014
Genome Biol
PMCID: 4232638
PMID: 25348012
DOI: 10.1186/s13059-014-0484-1

[…] [], protein variation effect analyzer (provean) [], functional analysis through hidden markov models (fathmm) [], variant effect scoring tool (vest) [], mutationtaster [], cancer driver annotation (candra) [], and others []. additionally, chasm, fathmm, and candra were developed explicitly to differentiate mutations that are likely to constitute cancer drivers from passengers. in particular, […]


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CanDrA institution(s)
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
CanDrA funding source(s)
This work was supported in part by the National Institutes of Health [grant number 1R01CA172652, CA168394, CA083639, CA143883, UL1TR000371 and 1U01CA180964]; the MD Anderson Cancer Center Sheikh Khalifa Ben Zayed Al Nahyan Institute of Personalized Cancer Therapy and the National Cancer Institute Cancer Center Support Grant [P30 CA016672].

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