When you are working on a Github repository with Jupyter Notebooks (ipynb), it is very likely that you only want to track the scripts by git, instead of tracking all the executed results. If you ju...

In our institute, we have a few Ubuntu servers that we want to monitor. In order to monitor these servers, we will use Prometheus and Grafana. Here are the steps to install and configure Prometheus...

Bioinformatics is an interdisciplinary field which is hard to define the boundaries. It combines biology, genomics, statistics, computer science and machine learning or artificial intelligence. As ...

“If the only tool you have is a hammer, you tend to see every problem as a nail.” Abraham Maslow We spend our whole lives learning how to solve problems, but there is a risk if we have only a few...

Let’s delve deeper into each of these distance measures to provide a more thorough understanding: Euclidean Distance: This distance metric is derived from the Pythagorean theorem a...

Sometimes the editors of the journal may ask for some statistics for the raw data. Here I just note some codes for them. Total number of sequenced reads Execute this command in the directory wher...

Various NGS technologies are able to profile gene expression, but how to make them comparable is another question. There are two levels of comparability: Within-sample comparability (across gen...

This is a note on how to generate code chunks in Rmd by looping through the data. ```{r, echo=FALSE, results='asis', warning=FALSE, message=FALSE} for (i in 1:50) { cat("\n### ", msig_gsea$path...

Problem I installed R in the conda environment and use RStudio Server to code R on an Ubuntu server. I have set all the environmental variables for Renv, but I still encounter the issue below some...

In RNA-seq experiments, External RNA Controls Consortium (ERCC) spike-in controls play a crucial role in assessing assay performance, monitoring technical variability, and quantifying gene expressi...