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CLONET specifications

Information


Unique identifier OMICS_07304
Name CLONET
Alternative name CLONality Estimate in Tumors
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Publication for CLONality Estimate in Tumors

CLONET in publications

 (8)
PMCID: 5539963
PMID: 28781886
DOI: 10.1038/npjgenmed.2016.19

[…] sections for assessing sample quality and neoplastic content, enrichment of tumour samples by macrodissection and evaluation of the run qc metrics. tumour purity is also assessed computationally by clonet, allowing more accurate estimation of tumour purity and ploidy in the tumour samples, especially in cases of low tumour burden. in addition, to make review of the exact-1 data effective […]

PMCID: 4777652
PMID: 26855148
DOI: 10.1038/nm.4045

[…] cohort and in cell lines (), suggesting that cyld loss alone may be insufficient but might cooperate with other alterations to promote ar- indifference. extending the computational framework of clonet, to assess allele specific copy number clonality (), we found both focal and broad copy-neutral or copy-aberrant loss of heterozygosity across our cohort () including focal allelic imbalance […]

PMCID: 4412223
PMID: 25897626
DOI: 10.3201/eid2105.141427

[…] showed an identical genotype in all 54 available isolates. this genotype was also identical to that of parasites isolated in 2010 in the loreto region of the peruvian amazon and closely related to clonet b, a parasite lineage previously reported in the amazon during 1998–2000. these findings are consistent with travel history of index case-patients. dna sequencing revealed mutations […]

PMCID: 4318437
PMID: 25315058
DOI: 10.1186/s13059-014-0464-5

[…] special issue we found a place for several excellent method articles: gabor marth and colleagues describe subcloneseeker (the clue is in the name!) [] and francesca demichelis and colleagues give us clonet [], both of which are designed for the analysis of clonality. shirley liu and colleagues [] describe a tool for the identification of differential methylation in single tumor samples. […]

PMCID: 3377589
PMID: 22723949
DOI: 10.1371/journal.pone.0039141

[…] and materials., funding: this work was supported by the austrian science fund (fwf, sfb f28), the austrian federal ministry of science and research (bm.w_fa, gen-au ii/iii “austromouse"), eu fp6 “clonet" (mrtn-ct-2006-035468) and “medrat" (lshg-ct-2006-518240). the funders had no role in study design, data collection and analysis, decision to publish or preparation […]


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CLONET institution(s)
Demichelis Lab - University of Trento, Italy

CLONET review

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the manual is simple, the input file description is very little, you must learn other software, such as segseq .It is very hard to understand the result files , because there is not more decrition.