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guigolab / lncATLAS

An easy to use web-based visualization tool to obtain useful information about expression localization of long non-coding class of RNAs
MIT License
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lncATLAS

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lncATLAS is an easy to use web-based visualization tool to obtain useful information about expression localization of long non-coding class of RNAs. It is easy to use by just searching your lncRNA of interest in the search box. You can also use ENSEMBL gene ids to select them. There are also some reference genes with a clear nuclear or cytoplasmatic expression profile.

Data

The data used and displayed in lncATLAS is directly obtained from GENCODE release V24 and it is available through our website in the download all data button from get raw data panel.

Measuring localisation

The RCI or Relative Concentration Index is a measure based on the logarithmic quotient between 2 fractions. For most of the plots, we use the CN RCI or Cytosolic / Nuclear expression in FPKMs.

This is a dynamic measure that permits a quantitative comparison between multiple genes and also permits analysing distributions of gene sets.

Citation

If you find lncATLAS useful for your work please cite us at:

Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Pulido TH, Guigo R, Johnson R. LncATLAS database for subcellular localization of long noncoding RNAs. Rna. 2017 Jul 1;23(7):1080-7.

Docker deployment

A Docker image with the latest released version of the application is available from the Docker Hub. It can be downloaded with this command:

docker pull guigolab/lncatlas

In order to build a docker image with a specific version of the application run the following command:

docker build -t lncatlas .

A new lncatlas image will now show at the top of the images list given by the command docker images.

The lncATLAS application resides in the folder /srv/shiny-server/ within the image. Credentials to access the backend database must be specified in a .mysqlconf file within the application folder. The shiny-server instance will run on port 3838 inside the container and a port has to be mapped on the host to connect to it. The follwing command runs a container in detached mode mapping port 80 on the host and mounting the .mysqlconf file as a volume:

docker run --name lncatlas -d -p 80:3838 -v /path/to/.mysqlconf:/srv/shiny-server/.mysqlconf lncatlas

Authors

This project has been carried out by Rory Johnson's Lab in the Department of Clinical Research (DCR) of the University of Bern and Roderic Guigo's Lab at the Centre for Genomic Regulation in Barcelona.

If you have questions or need further information please contact us at david.mas@crg.eu or open a issue in this repository.