Software Tools


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


F3UTER


Finding 3' Un-translated Expressed Regions (F3UTER) is a machine learning-based framework which leverages both genomic and tissue-specific transcriptomic features to predict previously unannotated 3'UTRs in the human genome. F3UTER was applied to transcriptomic data covering 39 human tissues studied within GTEx, enabling the identification of tissue-specific unannotated 3'UTRs for 1,513 genes.
Publication: Leveraging omic features with F3UTER enables identification of unannotated 3'UTRs for synaptic genes.


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GMSCA


GMSCA (Gene Multifunctionality Secondary Co-expression Analysis) is a software tool that exploits the co-expression paradigm to increase the number of functions and cell types ascribed to a gene in bulk-tissue co-expression networks. GMSCA was applied to 27 co-expression networks derived from bulk-tissue gene expression profiling of a variety of brain tissues and cell types, increasing the overall number of predicted triplets (gene, function, cell type) by 46.73%.
Publication: Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights.


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MitoNuclearCOEXPlorer


MitoNuclearCOEXPlorer is a web tool designed to allow users to interrogate and visualise key mitochondrial-nuclear relationships in multi-dimensional brain data. MitoNuclearCOEXPlorer uses brain regions data from GTEx v6p project.
Publication: Human brain mitochondrial-nuclear cross-talk is cell-type specific and is perturbed by neurodegeneration.


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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 (Nat Commun 12, 2076 (2021). doi: https://doi.org/10.1038/s41467-021-22262-5). 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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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.
Publication: CoExp: A Web Tool for the Exploitation of Co-expression Networks.


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AWS Integrity Check


Bash script to check the integrity of a set of local files uploaded to AWS S3.


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RytenLab API


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


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