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ritamtbsilvaritamtbsilva
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add new docker images and update gimm logo (#40)
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‎shinyproxy/templates/assets/img/logos/gimm.png‎

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‎shinyproxy/templates/index.html‎

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scStudio
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</b></h1>
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<!-- App Resources -->
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<p>
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<a href=""> </a>
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<p>
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<a href="https://www.biorxiv.org/content/10.1101/2025.04.17.649161v1">bioRxiv</a>
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</p>
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<!-- App Description -->
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</b> </h1>
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<!-- App Resources -->
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<p>
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<a href="https://rnajournal.cshlp.org/content/30/4/337.abstract">Paper</a>
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<a href="https://rnajournal.cshlp.org/content/30/4/337.abstract">Paper</a>
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<a href="https://github.com/DiseaseTranscriptomicsLab/betAS/tree/dev">GitHub</a>
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Tutorial
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</div>
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<!-- ------ missing card ------ -->
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<!-- ------ markeR ------ -->
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<div class="card reveal">
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<div>
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<h1> <b>
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<!-- Icon App -->
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<i class="fa fa-pencil" aria-hidden="true"></i>
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<!-- <img src="assets/img/markeR_icon.png" style="height: 1.2em; vertical-align: -0.15em;">-->
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<!-- Name App -->
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markeR
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</b></h1>
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<!-- App Resources -->
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<p>
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<a href="https://doi.org/10.1093/nargab/lqag057">Paper</a>
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<a href="https://doi.org/doi:10.18129/B9.bioc.markeR">Bioconductor</a>
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<a href="https://github.com/DiseaseTranscriptomicsLab/markeR/">GitHub</a>
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Tutorials:
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<a style="margin-right: 0em;" href="https://compbio.imm.medicina.ulisboa.pt/app_direct_i/markeR/_/tutorial/Tutorial_markeRShinyWebApp_shinyv0_99_7.pdf">[App]</a>
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<a href="https://diseasetranscriptomicslab.github.io/markeR/articles/markeR.html">[Package]</a>
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</p>
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<!-- App Description -->
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<p style="font-family: Syne Mono;"> Toolkit for evaluating gene sets as phenotype markers from gene expression data in R. </p>
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<!-- App link -->
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<div class="wrapper">
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<a class="button" href="/app/markeR" > Go <i class="fa-solid fa-chevron-right"></i> </a>
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</div>
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</div>
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</div>
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-->
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</div>
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<div class="w3-content w3-container w3-padding-24 reveal" id="developapps">
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<h1 class="w3-center">Other Apps in Development</h1>
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<div class="cards_grid " >
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<!-- ------ CREOLE ------ -->
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<!-- ------ CHARM ------ -->
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<div class="card ">
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<i class="fa-solid fa-align-left"></i>
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<i class="fa fa-diamond" aria-hidden="true"></i>
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CREOLE
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CHARM
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<a href="https://github.com/comprna/CREOLE">GitHub</a>
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<a href="https://github.com/DiseaseTranscriptomicsLab/CHARM/">GitHub</a>
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<p style="font-family: Syne Mono;"> Reference-free identification of open reading frames and encoded proteins from nanopore transcriptomic long reads </p>
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<p style="font-family: Syne Mono;"> Platform for studying how RNA-binding proteins regulate expression, splicing, and RNA binding through ENCODE data. </p>
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</div>
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<!-- ------ markeR ------ -->
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<i class="fa-solid fa-align-left"></i>
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markeR
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CREOLE
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<a href="https://github.com/DiseaseTranscriptomicsLab/markeR/">GitHub</a>
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<a href="https://github.com/comprna/CREOLE">GitHub</a>
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<!-- App Description -->
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<p style="font-family: Syne Mono;"> Toolkit for Evaluating Gene Signatures as Phenotype Markers in R </p>
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<p style="font-family: Syne Mono;"> Reference-free identification of open reading frames and encoded proteins from nanopore transcriptomic long reads. </p>
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</div>
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<div class="w3-content w3-container w3-padding-24 reveal" id="dockerimages">
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<h1 class="w3-center"> <i class="fa-brands fa-docker"></i> Docker Images</h1>
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At iMM, we have the opportunity of using Lobo, a multi-hundred node computer cluster. Lobo makes extensive use of Docker images, each a read-only templates that carries the instructions to build a Docker container. Containers are packaged applications that carry the necessary dependencies to allow running the program in every computer environment.
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At GIMM, we have the opportunity of using Lobo, a multi-hundred node computer cluster. Lobo makes extensive use of Docker images, each a read-only templates that carries the instructions to build a Docker container. Containers are packaged applications that carry the necessary dependencies to allow running the program in every computer environment.
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The following Docker images were developed by people in the Disease Transcriptomics team (in <span style="color: #18a986;"><strong>green</strong></span>, those under active maintenance).
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<div class="smallercard reveal" style="background-color: rgba(113, 213, 189, 0.25);">
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<div>
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<p style="font-family: Syne Mono;"> diseasetranscriptomicslab/ </p>
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<h5><b> <a href = "https://hub.docker.com/r/diseasetranscriptomicslab/charm/">charm</a> </b></h5>
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<p style="color:#a0a0a0;"> RBPs | gene-expression | alternative splicing </p>
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</div>
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</div>
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<div class="smallercard reveal" style="background-color: rgba(113, 213, 189, 0.25);">
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<div>
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<p style="font-family: Syne Mono;"> diseasetranscriptomicslab/ </p>
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<h5><b> <a href = "https://hub.docker.com/r/diseasetranscriptomicslab/marker/">marker</a> </b></h5>
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<p style="color:#a0a0a0;"> gene-expression | phenotypes </p>
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</div>
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</div>
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<div class="smallercard reveal" style="background-color: rgba(113, 213, 189, 0.25);">
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<div>
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<p style="font-family: Syne Mono;"> diseasetranscriptomicslab/ </p>
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<h5><b> <a href = "https://hub.docker.com/r/diseasetranscriptomicslab/voyager/">voyager</a> </b></h5>
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<p style="color:#a0a0a0;"> ageing </p>
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</div>
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</div>
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<div class="smallercard reveal" style="background-color: rgba(113, 213, 189, 0.25);">
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<div>
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<p style="font-family: Syne Mono;"> marianaferreira/ </p>
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<h5><b> <a href = "https://hub.docker.com/r/marianaferreira/betas">betas</a> </b></h5>
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<p style="color:#a0a0a0;"> alternative-splicing </p>
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</div>
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</div>
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<p style="font-family: Syne Mono;"> nunoagostinho/ </p>
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<p style="font-family: Syne Mono;"> nunoagostinho/ </p>
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<h5><b> <a href = "https://hub.docker.com/r/nunoagostinho/rmats4">rmats4</a> </b></h5>
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<p style="color:#a0a0a0;"> alternative_splicing </p>
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<p style="color:#a0a0a0;"> alternative-splicing </p>
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<p style="font-family: Syne Mono;"> nunoagostinho/ </p>
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<h5><b> <a href = "https://hub.docker.com/r/nunoagostinho/rmats">rmats</a> </b></h5>
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<p style="color:#a0a0a0;"> alternative_splicing </p>
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<p style="color:#a0a0a0;"> alternative-splicing </p>
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</div>
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</div>
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<div class="w3-xlarge w3-section">
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<!-- LOGOS -->
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<a href="https://imm.medicina.ulisboa.pt/pt-pt/" style="text-decoration: none;">
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<!--<a href="https://imm.medicina.ulisboa.pt/pt-pt/" style="text-decoration: none;">
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<img target="_blank" src="assets/img/logos/imm.png" alt="" height="50px">
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</a>-->
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<a href="https://gimm.pt" style="text-decoration: none;">
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<img target="_blank" src="assets/img/logos/gimm.png" alt="" height="80px">
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</a>
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<a href="https://www.embo.org/funding/fellowships-grants-and-career-support/young-investigator-programme/" style="text-decoration: none;">
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<img target="_blank" src="assets/img/logos/embo2.png" alt="" height="50px">

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