Software Tools


We have many tools and all of them are available on the following links:


vizER


vizER is a platform that enables the visualisation of individual genes for evidence of reannotation. We have two main publications associated to this app (Zhang et al. Science Advances 2020. doi: 10.1126/sciadv.aay8299) and (Chen et al. bioRxiv 2020. doi: https://doi.org/10.1101/2020.04.17.046441). The primary aim of vizER is to facilitate more accurate interpretation of variants and therefore, improve genetic diagnosis. vizER also allows to download complete, annotation-agnostic transcriptome definitions for 41 GTEx tissues.


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vizER - Docker


This is the Dockerized version of vizER.


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AWS Integrity Check


This is a bash script to assure the integrity of a set of local files previously uploaded into an AWS S3 bucket.


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RytenLab API


The RytenLab team also provides with a REST API, whereby it is possible to request different methods of the CoExp R framework.


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CoExp


CoExp is a framework for the generation, deployment, sharing and exploitation of co-expression networks as annotation models of genes and their role in transcription (Botía, J.A. et al. BMC Syst Biol 2017. doi: 10.1186/s12918-017-0420-6). This family of R packages can be separately downloaded from GitHub and also managed within the CoExp website, in which all CoExp R models are available to be accessed and used for your own research.


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CoExp - Docker


This is the dockerized version of CoExp. It's formed by two different docker images: one to contain the back-end of CoExp and the other one to contain the front-end of the CoExp website.


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