Welcome to the official Github repository of the CNVxplorer webserver available at http://cnvxplorer.com
The CNVxplorer manuscript is available on:
Requena, Francisco, et al. “CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients.” Nucleic acids research: gkab347.
- Overview
- Features highlight
- Availability
- Local installation
- Authors and contact
- License
- Disclaimer
- References
- News
CNVxplorer, a web server suited for the functional assessment of CNVs in a clinical diagnostic setting. CNVxplorer mines a comprehensive set of clinical, genomic, and epigenomic features associated with CNVs. It provides sequence constraint metrics, impact on regulatory elements and topologically associating domains, as well as expression patterns. Analyses offered cover (a) agreement with patient phenotypes; (b) visualizations of associations among genes, including those mediated by regulatory elements, and transcription factors; (c) enrichment on functional and pathway annotations; and (d) co-occurrence of terms across PubMed publications related to the query CNVs. A flexible evaluation workflow allows dynamic re-interrogation in clinical sessions
- Query a genomic interval, cytoband, or upload a file with multiple genomic regions.
- Explore CNV syndromes, pathogenic and non-pathogenic CNVs, disease variants (ClinVar, GWAS), and denovo variants (denovo.db) that overlap with the query CNV(s).
- Explore protein-coding genes targetted by the query CNV(s), including disease annotations from five reference sources (OMIM, ORPHANET, ClinGen, DECIPHER, and Genomics England PanelApp).
- Find regulatory elements overlapping within the genomic intervals of the query CNV(s) as well as their target genes (within or outside the query CNV(s) genomic intervals.
- Identify the genomic elements associated to the query CNV(s) with the closest phenotypic similarity to the patient’s clinical signs.
- Check the phenotype of KO experiments of the orthologous genes in mouse models.
- Perform gene-set level analyses covering functional and pathway enrichment, tissue specific expression and gene/protein interaction network analyses.
- Find PubMed articles related to the query CNV(s), analyse their keywork co-presence network, and filter articles by association with Mendelian diseases and genes.
CNVxplorer is publicly available at http://cnvxplorer.com
Detailed tutorials, comprehensive documentation, and a Frequently Asked Questions section are provided.
In addition, a stand-alone open-source R implementation with a shiny interface is offered in this repository, allowing its deployment as a private server through a Docker image without external dependencies. Instructions to locally deploy the application are provided in the next section.
# Note: the first session after the deployment is slower since the application loads all the data required
git clone https://github.com/RausellLab/CNVxplorer.git
mv CNVxplorer/Dockerfile .
docker build -t cnvxplorer . # The tag "cnvxplorer" is optional
docker run -d -p 3838:3838 cnvxplorer # -p (specify port) -d (detached mode)
# The port 3838 is optional. Please make sure you set a port not blocked by firewalls.
# If you change the port number (3838) by any other, make sure to set it in the Dockerfile
# (EXPOSE instruction)git clone https://github.com/frequena/cnvxplorer.git
cd cnvxplorer
gunzip -c local_data.RData.gz > local_data.RData
R -e 'load('local_data.RData')'
# Once you loaded the R environment with the files and functions
# comment the same two lines above in global.R so the app doesn't need
# to load the data every session but only once.
# Make sure you have all the packages installed
R -e 'shiny:runApp()'CNVxplorer has been developed by Francisco Requena and Antonio Rausell, at the Clinical Bioinformatics Laboratory of the Imagine Institute in Paris, France.
CNVxplorer is the result of a close collaboration with Prof. Valérie Malan and Prof. Serge Romana, from the Cytogenetics Service of the Necker Hospital for Sick Children (APHP) and the Bioinformatics Platform of the Imagine Institute headed by Patrick Nitschké.
Please address comments and questions about CNVxplorer to: * Francisco Requena - francisco.requena@institutimagine.org * Antonio Rausell - antonio.rausell@institutimagine.org
This project is licensed under the GNU General Public License 3 - see the LICENSE file for details
See the License for the specific language governing permissions and limitations under the License.
Copyright 2021 Clinical BioInformatics Laboratory - Institut Imagine
CNVxplorer or any document available from this server are distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express, implied, or statutory, including, but not limited to, any implied warranties of merchantability, fitness for a particular purpose and freedom from infringement, or that CNVxplorer or any documents available from this server will be error-free.
In no event will the Imagine Institute, the Clinical Bioinformatics lab, or any of its members be liable for any damages, including but not limited to direct, indirect, special, or consequential damages, arising out of, resulting from, or in any way connected with the use of CNVxplorer or documents available from it.
Requena, Francisco, et al. “CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients.” Nucleic acids research: gkab347. (Access)
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