conumee protocols

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conumee specifications

Information


Unique identifier OMICS_12411
Name conumee
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
Requirements
methods, stats, IRanges, GenomicRanges, DNAcopy, GenomeInfoDb, rtracklayer, BiocStyle, rmarkdown, knitr, RCurl, minfiData
Maintained Yes

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Maintainer


  • person_outline Volker Hovestadt <>

conumee in pipeline

2017
PMCID: 5756244
PMID: 29058119
DOI: 10.1007/s00401-017-1773-z

[…] clusters, k corresponding to the first downwards inflection in cumulative distribution function was used (online resource 2)., copy number analysis on 450k methylation data was carried out using the conumee r package. logr ratio thresholds of ± 0.15 were used as a cutoff to determine gains and losses., gene set enrichment analysis of methylation data was carried out using the gsameth function […]


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conumee in publications

 (8)
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004

[…] variants., methylation data from the illumina infinium humanmethylation450 beadchip was preprocessed using the minfi package in r. dna copy number was recovered from combined intensities using the conumee package with reference to methylation profiles from normal individuals provided in the copynumber450kdata package. we have used the heidelberg brain tumor classifier () […]

PMCID: 5736667
PMID: 29259247
DOI: 10.1038/s41467-017-02177-w

[…] were processed simultaneously using the parameters mentioned above., copy number variations were called for all jmml samples from the 450 k raw-intensity data using the bioconductor package “conumee”. the genomic identification of significant targets in cancer (gistic2) method was subsequently used to identify significant and recurrent copy number alterations based on the conumee raw […]

PMCID: 5673892
PMID: 29109526
DOI: 10.1038/s41467-017-01118-x

[…] generated calculating euclidean distance matrices based on all cpg sites on the array by the minimal evolution method using the fastme.bal function from the r package ape., the bioconductor package conumee was used to calculate copy number alterations from the intensities obtained from the 450k array (bin probe size was set to 5, rest of parameters set to default). gistic was then employed […]

PMCID: 5732792
PMID: 29262626
DOI: 10.18632/oncotarget.22021

[…] clustering the most differential probes (with 0,22 sd difference from the mean) were selected. to assess copy number variation (cnv) methylation data were implemented in the r/bioconducter packages conumee. intra-chromosomal breaks were calculated from the number of segments defined by the conumee package (blue horizontal lines in ). segments are defined as chromosomal regions with distinct […]

PMCID: 5756244
PMID: 29058119
DOI: 10.1007/s00401-017-1773-z

[…] clusters, k corresponding to the first downwards inflection in cumulative distribution function was used (online resource 2)., copy number analysis on 450k methylation data was carried out using the conumee r package. logr ratio thresholds of ± 0.15 were used as a cutoff to determine gains and losses., gene set enrichment analysis of methylation data was carried out using the gsameth function […]


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