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G-CNV specifications

Information


Unique identifier OMICS_11087
Name G-CNV
Alternative name GPU-copy number variation
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Parallelization CUDA
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Andrea Manconi

Publication for GPU-copy number variation

G-CNV citations

 (10)
library_books

Multi omics integration for neuroblastoma clinical endpoint prediction

2018
Biol Direct
PMCID: 5907722
PMID: 29615097
DOI: 10.1186/s13062-018-0207-8

[…] ault parameters. To avoid information leakage, feature filtering was performed on the TR data set and applied on both TR and TS data sets. For the integrative analysis, juxtaposed (juxt) datasets AG1-G/CNV-G, AG1-G/MAV-G and CNV-G/MAV-G were created concatenating AG1-G and CNV-G, AG1-G and MAV-G, and CNV-G and MAV-G respectively. […]

library_books

5 Hydroxymethylcytosine signatures in cell free DNA provide information about tumor types and stages

2017
Cell Res
PMCID: 5630676
PMID: 28820176
DOI: 10.1038/cr.2017.106

[…] ng but not limited to neurodegenerative diseases, cardiovascular diseases and diabetes. We envisage this strategy could be readily combined with other genetic and epigenetic-based cfDNA approaches (e.g., CNV analysis as we demonstrated) for increased diagnostic power. Our method represents the first enrichment-based genome-wide approach applied to cfDNA. The general framework of this method can be […]

library_books

lncRNA screen: an interactive platform for computationally screening long non coding RNAs in large genomics datasets

2017
BMC Genomics
PMCID: 5458484
PMID: 28583068
DOI: 10.1186/s12864-017-3817-0

[…] rmat where the fourth column corresponds to the ChIP enrichment score, calculated by MACS2 or any other peak calling tool. Any type of data that can be represented as segmented data in BED4 format (e.g. CNV or SNP data) is also supported as input to lncRNA-screen. For example, copy-number variation segments can be integrated by lncRNA-screen to identify lncRNAs located in recurrently amplified or […]

library_books

Sustained Subconjunctival Delivery of Infliximab Protects the Cornea and Retina Following Alkali Burn to the Eye

2017
PMCID: 5231904
PMID: 28114570
DOI: 10.1167/iovs.16-20339

[…] 0.9 and 0.99 “excellent agreement.” Intraclass correlation coefficient measurements were provided with 95% confidence interval. Mixed ANOVA was performed in datasets containing dependent variables (e.g., CNV, opacity scores, and corneal defect area) with fixed variables being time and treatment. Analyses were performed using the Statistical Package of Social Sciences (SPSS, IBM, NY, USA). Linear a […]

library_books

No Effect of Anodal Transcranial Direct Current Stimulation Over the Motor Cortex on Response Related ERPs during a Conflict Task

2016
Front Hum Neurosci
PMCID: 4974251
PMID: 27547180
DOI: 10.3389/fnhum.2016.00384

[…] (Miranda et al., ). In order to show specific effects of tDCS stimulation on motor processes, it is necessary to show that it specifically affects ERP components associated with response processes (e.g., CNV, LRP) and not ERP components associated with sensory and attention processes, such as the target-locked P300 (Picton, ; Linden, ; Polich, ). The P300 is a parietal positive peak that peaks at […]

library_books

Increased Proportion of Variance Explained and Prediction Accuracy of Survival of Breast Cancer Patients with Use of Whole Genome Multiomic Profiles

2016
Genetics
PMCID: 4937492
PMID: 27129736
DOI: 10.1534/genetics.115.185181

[…] iple omics with omic-by-omic interaction.In this study, we demonstrate how clinical information can be integrated with whole-genome omic data derived from several omic layers, including the genome (e.g., CNV), epigenome (METH), and transcriptome (miRNA and WGGE profiles). With some of the omics, we found statistically significant and, in some cases, substantial gains in predictive accuracy relativ […]

Citations

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G-CNV institution(s)
Institute for Biomedical Technologies, National Research Council, Milan, Italy; Department of Electrical and Electronic Engineering, University of Cagliari, Cagliari, Italy
G-CNV funding source(s)
The work has been supported by the Italian Ministry of Education and Research through the Flagship InterOmics (PB05) and HIRMA (RBAP11YS7K) projects, and the European MIMOmics (305280) project.

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