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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Volker Hovestadt

conumee citations

 (12)
call_split

Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

2018
Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004
call_split See protocol

[…] 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 () (molecularneuropatholog […]

library_books

RAS pathway mutation patterns define epigenetic subclasses in juvenile myelomonocytic leukemia

2017
Nat Commun
PMCID: 5736667
PMID: 29259247
DOI: 10.1038/s41467-017-02177-w

[…] 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 copy […]

library_books

Genome wide genetic and epigenetic analyses of pancreatic acinar cell carcinomas reveal aberrations in genome stability

2017
Nat Commun
PMCID: 5673892
PMID: 29109526
DOI: 10.1038/s41467-017-01118-x

[…] 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 to in […]

library_books

Pattern of p53 protein expression is predictive for survival in chemoradiotherapy naive esophageal adenocarcinoma

2017
Oncotarget
PMCID: 5732792
PMID: 29262626
DOI: 10.18632/oncotarget.22021

[…] d 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 copy […]

library_books

Comprehensive molecular characterisation of epilepsy associated glioneuronal tumours

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

[…] of 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 in th […]

library_books

Integrated Molecular Meta Analysis of 1,000 Pediatric High Grade and Diffuse Intrinsic Pontine Glioma

2017
Cancer Cell
PMCID: 5637314
PMID: 28966033
DOI: 10.1016/j.ccell.2017.08.017

[…] from Affymetrix SNP arrays was derived using the aroma.affymetrix and aroma.cn package. Combined log2 intensity data from Illumina 450K methylation arrays was processed using the R packages minfi and conumee. For sequenced samples, coverage of aligned reads was binned into known genes and exons with BEDTools and log2 ratios of median coverage in tumor and normal sequences were processed with in-ho […]

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