Recent content in Jeremy Selva on Personal website of Jeremy Selva
Introduction I have created this scrollytelling article below in Quarto about my life’s journey and reflection for 2025. It is best viewed on a desktop, rather than a mobile device. Here is the link https://jauntyjjs.github.io/reflection_2025/ to access it. The source code used to generate this reflection can be found in this GitHub page.
Here are the slides.
Here are the slides.
Here are the slides.
Here are the slides.
Here are the video and slides.
As diagnosis of CAD involves a costly and invasive coronary angiography procedure for patients, having a reliable PTP for CAD helps doctors to make better decisions during patient management. This ensures high risk patients can be diagnosed and treated early for CAD while avoiding unnecessary testing for low-risk patients. R package pretestcad helps to ensure that these PTP values can be…
Here are the video and slides.
Introduction I have created this scrollytelling article below in Quarto about my life’s journey and reflection for 2024. It is best viewed on a desktop, rather than a mobile device. Here is the link https://jauntyjjs.github.io/reflection_2024/ to access it. The source code used to generate this reflection can be found in this GitHub page.
Here is the link https://jauntyjjs.github.io/fertility_dashboard/ to view the simple dashboard made for the presentation. Here are the slides.
Table of Content Introduction Formal Debugging 🐛 in R Debugging your code traceback rlang::entrace and rlang::last_trace browser RStudio IDE Breakpoints and Error Handler Debugging other people’s code debug, undebug and debugonce options(error=recover) and trace Other Debugging Techniques Debugging Tutorial Resources Building Effective Docker 🐳 Images: R Edition Images and Containers…
Here are the slides.
Table of Content Introduction Decomposition Based Deep Learning Model For Forecasting Agricultural Commodity Prices with decompDL Modeling Antimicrobial Resistance Rate Data using DeβARMA Share your R with Quarto Enhancing the R Development Guide Making Better Error Messages with cli Connecting Shiny Apps to Chemotion-ELN One Container to Rule Them All Minimum Viable Good Practices for High…
Overview Reading data in formatted cell in excel can be really tricky. In this post, I will share six problematic formatted columns to read and share how I try to handle them. Data Set The data set can be found in this link: https://raw.githubusercontent.com/JauntyJJS/jaunty-blogdown/main/content/blog/2024-02-15-Tackling-Formatted-Cell-Data/sample_excel.xlsx Here is a peak view of the excel file…
Here are the video and slides. For this video, I was going through Chapter 18 of the book R4DS 2nd edition.
Here are the video and slides. For this video, I was going through Chapter 13 of the book R4DS 2nd edition.
Table of Content Introduction p-values What p-values cannot do What p-values can do Risk Scores for Cardiovascular diseases Correcting for Multiple or Recurrent Events Correcting for Multiple or Recurrent Events Correcting for Mortality Endpoints Correcting for both groups of outcomes Questions to ask regarding AI Where is the model What Information is used to build the model Has the model been…
Here are the video and slides. For this video, I was going through Chapter 2 of the book R4DS 2nd edition.
Table of Content Introduction Day 1 Application of R and Shiny in Digital Marketing Intelligence Data Storytelling in R Contributing to R Packages Univariate Bayesian Approach to Fine-mapping Genes Web Scraping, Text and Network Analysis in R Day 2 Tidymodels in Medicine Partial Verification Bias Correction Integrating R with Web Applications with OpenCPU Bibliometrics Analysis in R Modeling…
lancer is an R package used to validate if a curve is linear or has signal suppression by statistical analysis and plots. Here is the link to the documentation
Here are the video and slides. I am the second speaker it begins at 16:20
I initially wanted to create for myself a record of some Awesome Lists which are useful in the field of bioinformatics and computational biology and create a post here. However, upon seeing this twitter post, I decided to do things differently and attend the meetup instead with an open mind. After all, it is better to have someone to verify if what I do is meaningful. Join our meetup to learn how…
Here are the video and slides. Xaringan Slide Template by Sharla Gelfand
Introduction Time flies since the last conference that I have attended. I am fortunate to be given a chance to attend the R/Medicine 2022 Conference and give a lightning talk as well. The general goal of the R/Medicine Conference is to help practitioners in clinical and medicine sciences improve the quality of their research workflow with the use of R based tools. The focus is mainly on the…
Introduction This is a continuation about my learning journey in R/Medicine 2022. This section covers Day 3 and 4 of the conference. As the videos of the presentation are not available, the writings made are based on my memory. If there are any mistakes, kindly let me know. Day 3 Keynote: Quarto Day 3 of the conference started with a keynote, presented by JJ Allaire, founder of RStudio, which soon…
Here are the videos. For this video, I was going through the contents of the book. For this video, I was going through the lab session. Here are the slides. Here is the lab session. Xaringan Slide NHS-R Theme Template by Silvia Canelón Many thanks to Irene Vrbik’s blog for helping me learn more about Xaringan.
Introduction I have created this html report in Quarto to show how to create some interactive quality control plots using plotly and display as a trellis using trelliscopejs. The source code used to generate this report can be found in this GitHub page. Background Here is some background knowledge about the use of the quality control (QC) plots, for example, the injection sequence plot and the…
Introduction In this narrative, I will continue sharing my learning journey during Day 4 of useR! 2022 Virtual Conference. Day 4 First Keynote: Junior R-core Experiences Day 4 of the conference started with a keynote by the R Core Team. The keynote was led by Sebastian Meyer who had recently joined the R Core team. The first part of the presentation was about a summary of the major changes in R…
Introduction In this narrative, I will continue sharing my learning journey during Day 3 of useR! 2022 Virtual Conference. Day 3 First Keynote: afrimapr The first keynote was by the afrimapr project team. The project aims is to use R as a building block for many things such as better management of data realted to Africa, creation of open source analytical tools to analyse and provide insights…
Introduction The useR! 2022 Virtual Conference has provided me to new things about R as well as an opportunity to meet new people along the way. Here is a narrative of my learning journey in the conference for Day 1 and Day 2. Day 1 I have attended two workshops this year titled Introduction to Dimensional Reduction in R and Regression Modeling Strategies. Introduction To Dimensional Reduction In…
Introduction Docker 🐳 (1) has been gaining in popularity in the academic field to ensure scripts that are used to run on research data can be easily opened and explored by others. A picture friendly introduction of Docker can be found in this Devopedia webpage. As someone who has just started to learn how to use this in a non-computing academic lab, the onboarding learning curve for Docker just…
Here are the videos. For this video, I was going through the contents of the book. For this video, I was going through the lab session. Here are the slides. Here is the lab session. Xaringan Slide NHS-R Theme Template by Silvia Canelón Many thanks to Irene Vrbik’s blog for helping me learn more about Xaringan.
Introduction Finding resources to learn and write VBA code in Excel is relatively simple. Guru99 and DevTut are good places to start. As I have gotten more familiar with the programming, I then started to look at best code practices for VBA code in Excel. Here are some web resources that was helpful to me: Corporate Finance Institute’s Tips for Writing VBA in Excel Corporate Finance…
Introduction In this blog, we continue the process of cleaning up these lipid annotations that my workplace uses Given Name Clean Name For Annotation Precursor Ion Product Ion DG 32:0 [-16:0] DG 16:0_16:0 586.5 313.3 DG 36:1 [NL-18:1] DG 18:1_18:0 640.6 341.3 TG 54:3 [-18:1] TG 18:1_36:2 902.8 603.5 TG 54:3 [NL-18:2] TG 18:2_36:1 902.8 605.5 TG 54:3 [SIM] TG 54:3 902.8 902.8 This is so that they…
Here are the videos. I am the second speaker in this video and it begins at around 33:18. For this video, I was going through the lab session Here are the slides. Here is the lab session. Xaringan Slide NHS-R Theme Template by Silvia Canelón Many thanks to Irene Vrbik’s blog for helping me learn more about Xaringan.
Introduction In this blog, I will introduce another set of lipid annotations that my workplace uses that require to be cleaned up and modified so that they can be processed by lipid annotations converter tools like Goslin (1), (2) and RefMet (3). R Packages Used library('rgoslin') library('reactable') library('flair') library('readr') library('magrittr') library('stringr') library('dplyr')…
Introduction Despite efforts made to unified lipids shorthand notations and the rise of software dedicated to standardise lipid annotations, lipid names still remains diverse. This is due to limited ways lipid software may label a lipid and/or researchers’ personal preferences to annotate them. Here, I would like to highlight some lipid annotations that my workplace uses and show how to modify…
Here are the video and slides. I am the second speaker in this lightning talk and it begins at 9:40. Images by Amonrat Rungreangfangsai Xaringan Slide Template by Sharla Gelfand
Introduction I have created this post to explain how the number displayed in the BioPAN software are calculated using a small dataset as an example. Below is a preview of how it look like. About BioPAN BioPAN (1) is a tool found in LIPID MAPS designed to automate biosynthetic pathway analysis of lipids. Below is a YouTube video on how to use BioPAN. Source Code The source code of this post can be…
MSOrganiser is created to provide users a convenient way to extract and organise MRM transition names data exported from mass spectrometry software into an Excel or csv file in a few button clicks. With the addition of the MSTemplate_Creator, the software is also able to normalize the peak area with respect to the internal standard’s peak area and calculate the concentration of the analytes.
MSTemplate_Creator is an excel macro file created to provide users friendly interface to take in MRM transition names data exported directly from mass spectrometry software to create several annotation templates suited for automated data processing and statistical analysis.
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