How to learn Bioinformatics?
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 ...
Genomics AI
A hammer and a nail.
“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...
The Significance of Distance Measures in AI and ML Algorithms
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...
Statistics for NGS data
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...
How to normalize read counts for RNA-Seq?
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...
Generate chunks of codes in Rmd
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...
An issue in R in compiling packages
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...
Understanding ERCC Controls in RNA-seq Experiments
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...
Configuration of renv environment with R in conda env
It is not a trivial task to manage R environment. Here is my note for configuration of renv for Seurat analysis. Because conda env cannot handle all R packages properly and renv cannot manage diff...
Conflict in htmltools versions between Seurat and renv
renv (version 1.0.3) uses htmltools version 0.5.6.1, but Seurat v5 uses htmltools version 0.5.7. When I initiate a renv project and then install Seurat, I encounter an issue as: /opt/miniconda3/en...