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Building interactive dashboards with Streamlit (Part I)

Python is often used in back-end programming, which builds functionality in web applications. For instance, Python can be used to connect the web to a database, so that users can query information. By adding the backend components, Python turns a static webpage into a dynamic web application, where users can interact with the webpage based […]

The transcriptional landscape of age in human peripheral blood

Chronological age is a major risk factor for many common diseases including heart disease, cancer and stroke, three of the leading causes of death. Previously, APOE, FOXO3 and 5q33.3 were the only identified loci consistently associated with longevity. The discovery stage included six European-ancestry studies (n=7,074 samples) with whole-blood gene expression levels (11,908 genes). The […]

Streamlit: My recommended tool for data science app development

Streamlit is a web application framework that helps in the building and development of Python-based web applications to share data, build data dashboards, app development and even build machine learning models. In addition, developing and deploying Streamlit apps is amazingly quick and versatile, allowing the development of simple apps in a few hours. In fact, […]

My experience with Voilà and Streamlit for building data dashboards

The role of data scientist is clear: To analyse the data, plot visualisation graphs and consolidate the findings into a report. However, with greater interest in deeper understanding of big data and urgent need for more novel tools to gain insights from biological datasets, there is a growing interest in employing data engineers. Their roles […]

Choosing the best machine learning model with LazyPredict

The idea of using machine learning models to make predictions is attractive. But a challenging question remains: There are so many machine learning models out there, but which model is most suitable? Which model should I start exploring? Should I fit every single model that I have learnt and try my luck and see which […]

Gene Expression Patterns of Dengue Virus-Infected Children from Nicaragua Reveal a Distinct Signature of Increased Metabolism

Identifying signatures of host genome-wide transcriptional patterns can be a tool for biomarker discovery as well as for understanding molecular mechanisms and pathophysiological signatures of disease states. In this study by Loke et al., transcriptional profiling analysis of pediatric patients from Nicaragua with a predominantly DENV-1 infection was performed, and the gene signatures between healthy, […]

The fundamentals of machine learning

Machine learning is a hot topic in data science, but few people understand the concepts behind them. You may be fascinated by how people get high paying jobs because they know how to execute machine learning, and decide to delve deeper into the topic, only to be quickly intimidated by the sophisticated theorems and mathematics […]

Systems Vaccinology Identifies an Early Innate Immune Signature as a Correlate of Antibody Responses to the Ebola Vaccine rVSV-ZEBOV

Predicting and achieving vaccine efficacy remains a major challenge. Here, Rechtien et al used a systems vaccinology approach to disentangle the early innate immune responses elicited by the Ebola vaccine rVSV-Zaire Ebola virus (ZEBOV) to identify innate immune responses correlating with Ebola virus (EBOV)-glycoprotein (GP)-specific antibody induction. Of note, this replication-competent recombinant vaccine candidate is based […]

Making interactive and executable notebooks/dashboards with Lux and Voilà packages

As described in my previous blog posts, pair plots and correlation matrices are useful to quickly analyse relationships between multiple variables. However, when analysing the datasets with more than 10-20 variables, these analysis methods have their limitations. One critical limitation is the difficulty in assessing the effects of 2 or more categorical variables. Another is […]

A 20-Gene Set Predictive of Progression to Severe Dengue

The gene signatures predictive of severe dengue disease progression is poorly understood. The study by Robinson et al., utilise 10 publicly available datasets and divided them into 7 “discovery” and 3 “validation” datasets. In the discovery datasets, a total of 59 differentially expressed genes (FDR < 10%, effect size > 1.3-fold) was detected between patients […]

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