Computational biology and genomics
I guess by now you have probably heard about DeepSeek. If in the extremely unlikely event that you have come across this post before reading about DeepSeek, please go look them up. When I first heard about them and their amazing LLM models, the first thing I wanted to do was to try them out!…
In April 2023, I had tried to get GPT4All, a tool to run LLMs locally, to work on one of my servers running Debian 12 at home without avail; I just couldn’t get it to install. (I have to say, GPT4All does look much more developed now compared to back then.) So when I learned…
The Gene Set Variation Analysis (GSVA) is another popular analysis method for bulk RNA-seq data. GSVA differs from Gene Set Enrichment Analysis (GSEA) in that it can estimate gene set enrichment within a single sample. GSEA typically uses results from a differential expression analysis, which requires multiple samples, to determine whether there is an enrichment…
The {GenomicDataCommons} Bioconductor package provides basic infrastructure for querying, accessing, and mining genomic datasets available from the Genomic Data Commons (GDC). The About the GDC webpage provides a brief description of the program: The Genomic Data Commons (GDC) is a research program of the National Cancer Institute (NCI). The mission of the GDC is to…
The Molecular Signatures Database (MSigDB) is a nice resource containing various gene sets designed for use in Gene Set Enrichment Analyses (GSEA) and its variants. It was co-developed with the GSEA by the Broad Institute and is still maintained by them; you can read more in the classic paper: Gene set enrichment analysis: A knowledge-based…