CNTools specifications

Information


Unique identifier OMICS_02061
Name CNTools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.37.0
Stability Stable
Requirements
methods, stats, tools, R(>=2.10), genefilter
Maintained Yes

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Documentation


CNTools in publications

 (20)
PMCID: 5905168
PMID: 29665859
DOI: 10.1186/s13058-018-0951-9

[…] on the basis of resulting absolute copy number profile and after filtering for regions with < 50 snp variations. recurrent alterations (cnv, loh) among the cohort were obtained using the cntools r package (version 1.24.0; r foundation for statistical computing, vienna, austria) and a homemade script. in order to find inherent grouping structure, hierarchical clustering was performed […]

PMCID: 5829240
PMID: 29487377
DOI: 10.1038/s41598-018-22126-x

[…] used to assist the determination of the cutoffs. used cutoffs for the samples are given in the supplementary table . the frequently altered regions in the cohort were determined using the r packages cntools and cghmcr. losses seen in more than 20%, and gains in more than 25% of the samples were included for further analyses (supplementary fig.  and supplementary table ). after determining […]

PMCID: 5777739
PMID: 29383127
DOI: 10.18632/oncotarget.22928

[…] by the sum of all segment lengths., a reduced segment matrix was extracted from segmented copy number data for each ccle and tcga-skcm sample and was used to calculate mean copy-number per gene with cntools []. the cntools algorithm aligns segments across samples, and genes that fall within an overlapping segment are assigned the mean of the probe log2 ratios within that segment. genome […]

PMCID: 5564726
PMID: 28415743
DOI: 10.18632/oncotarget.16178

[…] a segment was set as (0.2 and −0.2), and for the cna evaluation of genes, we chose more strict thresholds to enhance the classification power, which is 0.3 and −0.2 in subsequent analysis. then the “cntools” (version 1.22.0) transformed the segment information into a reduced segment matrix (segments as rows and samples as columns), enabling a convenient calculation of the cna frequency […]

PMCID: 5400640
PMID: 28423542
DOI: 10.18632/oncotarget.15777

[…] euclidean distance matrices were based on log2 ratios (i.e. tumor dna versus matched germline dna), where the segmentation data was converted to a gene by sample matrix using bioconductor r package ‘cntools’ []., pearson’s correlation coefficient was calculated to estimate the similarity between methylation and genomic distances matrices. a linear regression was used to determine […]


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