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Oncotree specifications

Information


Unique identifier OMICS_09055
Name Oncotree
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
Version 0.3.3
Stability Stable
Requirements
R(≥2.10), lattice, boot
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Aniko Szabo

Publication for Oncotree

Oncotree citations

 (8)
library_books

Genomics alterations of metastatic and primary tissues across 15 cancer types

2017
Sci Rep
PMCID: 5643378
PMID: 29038591
DOI: 10.1038/s41598-017-13650-3

[…] onco-types. most onco-types were classified into 15 categories (detailed information regarding sample, onco-type, and primary and metastatic tissue number are shown in fig.  and table ) according to oncotree (http://oncotree.mskcc.org/oncotree/), as non-small cell lung cancer (nsclc), breast cancer (idc), colorectal cancer (crc), prostate cancer (prad), bladder cancer (blca), glioma, ovarian […]

library_books

Somatic cancer variant curation and harmonization through consensus minimum variant level data

2016
Genome Med
PMCID: 5095986
PMID: 27814769
DOI: 10.1186/s13073-016-0367-z

[…] for describing cancers []. several cancer-focused ontologies are available, such as national cancer institute (nci) thesaurus [], a set of encoded terms to describe cancers and tissue pathology, and oncotree, a set of 519 tumor types in 32 tissues []. oncotree includes the nci thesaurus code for each cancer type. through the nci term browser, the nci thesaurus codes can also be related […]

library_books

The Occurrence of Genetic Alterations during the Progression of Breast Carcinoma

2016
Biomed Res Int
PMCID: 4848409
PMID: 27190992
DOI: 10.1155/2016/5237827

[…] flexible since they can represent multiple pathways at the same time []. various bioinformatics software programs have been proposed for the construction of oncogenetic tree including trap [] and oncotree []., in this paper, we construct two oncogenetic trees based on independent models based for human breast carcinoma. in the distance-based oncogenetic tree construction, the state […]

library_books

Clinical and Molecular Characterization of Brazilian Patients Suspected to Have Lynch Syndrome

2015
PLoS One
PMCID: 4593564
PMID: 26437257
DOI: 10.1371/journal.pone.0139753

[…] mutation-positive and negative families, providing, for the first time, an initial genetic and clinical description of families suspected of having ls within a cohort in brazil., the study used the oncotree database of the hereditary colorectal cancer registry of the pelvic surgery department of ac camargo cancer center (são paulo, brazil). the analyzed families were selected according […]

library_books

Inferring Tree Causal Models of Cancer Progression with Probability Raising

2014
PLoS One
PMCID: 4191986
PMID: 25299648
DOI: 10.1371/journal.pone.0108358

[…] is the asymmetric temporal priority measured by rate of occurrence. this implicit form of timing assumes that, if occurs more often than , then it likely occurs earlier, thus satisfying , an oncotree is the rooted tree whose total weight (i.e., sum of all the weights of the edges) is maximized, and can be reconstructed in steps using edmond's algorithm . by construction, the resulting […]

library_books

INCT in oncogenetics focusing on hereditary breast colorectal carcinoma syndrome

2013
BMC Proc
PMCID: 3624113
PMID: 24764476
DOI: 10.1186/1753-6561-7-S2-K19

[…] among brazilians. the department of oncogenetics of the ac camargo hospital was created in 2000 and since then, more than 4,500 patients and family members have received genetic counseling. the oncotree software is used to monitor family history data. in the ac carmago hospital peripheral blood dna samples of patients with hereditary cancer or family history or familial aggregation […]


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Oncotree institution(s)
Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA

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