Introduction

Breast cancer is one of the most important morbidity and mortality cases around the world. In 2022, 2.3 million women were diagnosed with breast cancer and about 670,000 died from the disease, according to the World Health Organization.

Traditional breast cancer treatment with chemotherapy may be complicated …

Introduction

Sometimes, some computations can be carried out in parallel. Certain large tasks can be divided into independent ones, allowing them to be solved at the same time, rather than waiting for each task to be solved sequentially.

I find the native R parallel functions such as mclapply(), or those …

Introduction

Genomics is undoubtedly a complex science. The human genome is huge, with more than 3 billion base pairs, about 20,000 protein-coding genes, several millions of variants, and many more interesting characteristics. The visualization of genomic/omics data is challenging due to the sheer volume of information. Circular plots …

Introduction

reticulate is an R package that allows interoperability between R and Python. I recently discovered this package, and I have been excited to efficiently run Python scripts inside an R session, bringing the best of both worlds.

In this post, I will demonstrate reticulate with two scripts. First, I …

Introduction

Shiny is a R package developed and maintained by the RStudio team. With Shiny, anyone can build interactive web apps to help data visualization. Here I present a simple template of an interactive Brazilian map displaying fictitious allelic frequencies with samples sizes across the country. It is a useful …

Introduction

In my previous post I demonstrated how to organize the CGC prostate cancer data to a format suited to differential expression analysis (DEA).

Nowadays, DEA usually arises from high-throughput sequencing of a collection (library) of RNA molecules expressed by single cells or tissue given their conditions upon collection and …

Introduction

In my previous post I demonstrated how to obtain a prostate cancer dataset with genomic information in the form of gene expression quantification and created a local PostgreSQL database to hold the data.

Here, I will use R to connect to the PostgreSQL database, retrieve and then prepare the …

Introduction

On December 2019, reports from severe acute respiratory syndrome in Wuhan, China, were linked to a novel coronavirus, now known as SARS-CoV-2, and the disease it causes was termed coronavirus disease 2019 (COVID-19).

The World Health Organization declared the COVID-19 outbreak a Public Health Emergency of …