https://imm.medicina.ulisboa.pt/bioinformaticsmatters/ 2026-04-26T02:03:44+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/ https://imm.medicina.ulisboa.pt/bioinformaticsmatters/lib/exe/fetch.php?media=favicon.ico text/html 2020-10-15T13:48:14+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=1st_cbbday&rev=1602762494&do=diff Programme under construction. text/html 2024-07-24T12:23:35+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=betas&rev=1721816615&do=diff betAS intuitive analysis and visualisation of differential alternative splicing by Mariana Ascensão-Ferreira marianaascferreira@medicina.ulisboa.pt and Rita Martins-Silva rita.silva@medicina.ulisboa.pt betAS is a user-friendly Shiny-based Web App and R package that allows intuitive analysis and visualisation of differential alternative splicing text/html 2020-07-16T13:19:09+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=ctrap&rev=1594898349&do=diff cTRAP Identification of candidate causal perturbations from differential gene expression data by Nuno Agostinho nunoagostinho@medicina.ulisboa.pt cTRAP is an R package designed to compare differential gene expression results with those from known cellular perturbations (such as gene knockdown, overexpression or small molecules) derived from the Connectivity Map (CMap; Subramanian et al., Cell 2017). Such analyses allow not only to infer the molecular causes of the observed difference in gene… text/html 2021-07-19T13:38:05+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=faqs&rev=1626694685&do=diff Q: Are you a Bioinformatics Facility/Unit at iMM? No. We are a Research Community at iMM. See more about what we do here. Q: Can you analyse my data? No. We can help to guide you in finding the right resources to analyse your data. Check if our learning section can help you. text/html 2020-07-13T18:15:25+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=funding&rev=1594656925&do=diff GenomePT GenomePT is a consortium of Portuguese research infrastructures, including iMM, that aims to provide sequencing and bioinformatics services for genome projects. GenomePT is integrated in the Portuguese Roadmap of Research Infrastructures. The GenomePT iMM Node supports the Bioinformatics Matters text/html 2021-07-19T11:38:17+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=how&rev=1626687497&do=diff Our Mission Our work is focused on three main pillars: sharing, training and networking. sharing Share your work We are witnessing an exponential increase in the creation of new bioinformatics tools, workflows, R packages, and Docker images, amongst others. To ensure a sustainable evolution, we need to text/html 2020-07-13T18:16:22+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=join&rev=1594656982&do=diff Share with us ...because we definitely want to share with you! :-P Send us your ideas/thoughts/doubts, and ask us to include you in our mailing list. You will receive updated news on our activities! Be part of BIOINFORMATICS MATTERS Ok, let's face it: this community is all about sharing! But if sharing is not enough for you, feel free to text/html 2022-12-05T16:08:34+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=networking&rev=1670252914&do=diff Events CBBS at iMM The Computational Biology and Bioinformatics Seminars, aka CBBS, started in 2012 as an initial effort to bring together iMM researchers using computational methods and resources in different areas of biomedical research. The CBBS are open to everyone, including scientists without a computational background that would like to learn more about this area. Each seminar will be associated with an accessibility score, that will be timely disclosed for each seminar: text/html 2020-07-16T13:19:25+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=psichomics&rev=1594898365&do=diff Psichomics Graphical application for alternative splicing quantification and analysis by Nuno Agostinho nunoagostinho@medicina.ulisboa.pt Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) project, Sequence Read Archive (SRA), and user-provided data. text/html 2024-07-24T12:31:35+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=sharing&rev=1721817095&do=diff Tools All Bioinformatics tools listed below are work developed by researchers at iMM. The respective authors are solely responsible for their contents and functionality, so feel free to contact them. Please get in touch if you want to help populate the lists below by sharing the tools you have developed. text/html 2021-07-20T11:58:13+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=sidebar&rev=1626775093&do=diff training sharing networking text/html 2021-11-24T10:43:38+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=start&rev=1637747018&do=diff Welcome to the Bioinformatics Matters community at iMM! We are a Research Community born due to the need of gathering all iMMers with an interest in Bioinformatics. Attention, all bioinformaticians, computational biologists, software developers, data scientists, statisticians, wet-lab biologists dealing with “omics” data, and all the other researchers working in or just enthusiasts or curious about Bioinformatics-related topics – text/html 2023-10-23T17:43:18+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=team&rev=1698075798&do=diff Core Marta Bica ana.bica@medicina.ulisboa.pt CAML PhD Student (FMUL), MSc. in Bioinformatics and Computational Biology (FCUL/UL), and BSc. in Health Sciences (UL) NMorais Lab - FCT Fellowship (former GenomePT Fellow) Rita Silva rita.silva@medicina.ulisboa.pt LisbonBioMed PhD Student (FMUL), MSc. in Biomedical Engineering (IST/UL), and BSc. in Engineering Sciences - Biomedical Engineering (IST/UL) text/html 2021-07-21T14:36:56+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=training&rev=1626871016&do=diff Learning Docker and Lobo Docker is a platform created to facilitate the use of applications through so-called containers. Docker images are read-only templates that carry 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. text/html 2024-07-24T12:32:21+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=voyager&rev=1721817141&do=diff voyAGEr Web interface for the analysis of age-related gene expression alterations in human tissues by Arthur L Schneider, Rita Martins-Silva rita.silva@medicina.ulisboa.pt and Alexandre Kaizeler alexandre.afonso@medicina.ulisboa.pt voyAGEr is a web interface for the analysis of age-related gene expression alterations in GTEx human tissues. The app leverages RNA-seq datasets from the GTEx project (Lonsdale et al., 2013), encompassing tissue samples from hundreds of donors aged from 20 to 70… text/html 2020-07-13T17:57:52+02:00 https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=what&rev=1594655872&do=diff We are a Research Community We are a community of iMMers aiming to include all bioinformaticians, computational biologists, software developers, data scientists, statisticians,wet-lab biologists dealing with “omics” data and all the others researchers working in or just enthusiasts or curious about Bioinformatics-related topics. We believe that bringing you together with colleagues with common interests can make