CNVision is a small, simple application designed to simplify CNV analysis of Illumina genotyping data.
It will simplify all stages of predicting and analyzing CNVs, from running prediction algorithms and combining their results to visualizing the raw data and designing qPCR primers for confirmation.
CNVision is a program that analyses whole genome genotyping array data, in order to predict CNVs, locate and visualize them. CNVision provides a graphical user interface, which simplifies all stages of CNV prediction and detection.
CNVision can be used for predicting novel CNVs and finding CNVs in known loci, and for assessing the quality of genotyping array data.
CNVision Features:
CNVision is designed to be intuitive and simple. Its graphical user interface is very simple and can be used without any knowledge of CNV prediction.
CNVision is able to import data from different file types, such as text files or in/excel worksheets, while providing the ability to visualize the data in the same file or save it to a file.
CNVision uses internal or online databases in order to provide a comprehensive source of CNVs. The software can import data from other databases if they are listed in the CNVision preferences.
CNVision is able to use all currently available whole genome genotyping arrays and is compatible with both Illumina and Affymetrix arrays. CNVision will estimate the size of CNVs and will align them to the genome.
CNVision has a number of built-in algorithms, which can be used to identify CNVs. CNVision can make use of multiple algorithms to make a final prediction of CNVs.
CNVision is compatible with both copy number data and sequence alignment data. CNVision can also export data as fasta files and visualized as heatmaps.
CNVision can export results to a csv-file or csv-format for use in spreadsheets, databases or other software.
CNVision can plot predicted CNVs and visualize the data in two different ways. In the first plot, called a dendrogram, there is a color gradient that represents the degree of confidence in the predicted CNV. In the second plot, called a heatmap, the results from all the algorithms can be visualized as one graph.
CNVision includes a large number of algorithms, all of which can be run in batch mode.
CNVision is designed to be compatible with other software.
CNVision can output data as a csv-file or csv-format.
CNVision will align CNVs to the genome and save the result
CNVision is a simple application designed to assist in the creation of custom reports that summarize and visualize Illumina genotyping data.
CNVision can be used to run a wide variety of analysis algorithms, and combine their results into an ordered list of predicted CNVs, as well as displaying the raw data in a visual chart, and visualizing the data on a map.
Supported data sources:
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Reads FASTQ files with alignments.
Calls CNVs on the reads.
Collates the CNVs by overlaps and provides an interactive interface.
Has an option to compare the raw data with other CNVs by plotting in the UCSC Genome Browser.
Category:BioinformaticsQ:
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CNVvision is a simple application to analyze Illumina genotyping data. It has been designed to make it easy to compare CNVs predicted by different tools and combine their results.
Basic functions:
1. Read raw input data and store them as binary data.
2. Predict CNVs from the input data with multiple prediction methods.
3. Combine CNV results of different methods.
4. Analyze CNV regions.
5. Convert CNV regions to gene lists.
6. View CNV predictions on the genome.
7. View CNVs predicted for a selected region.
8. Export predicted CNVs to bam/fasta and/or vcf files.
9. Analyze data by plotting CNVs in the genome.
10. Perform t-test for CNV regions.
Installation:
1. Unzip the archive.
2. Open the CNVvision folder.
3. Run “cnuvision.exe” to launch CNVvision.
CNVvision is a part of the SnpEff tool.
Licence:
CNVvision is released under the GPL 2.0 licence. It may be used without restrictions.
Contact:
If you use CNVvision or have questions about using it please contact
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