Computational biology and genomics
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…
For converting Ensembl Gene IDs to gene symbols, using biomaRt is often recommended and indeed it is what I typically use. However, recently I needed to use Ensembl version 112 and could not get {biomaRt} to work with this specific version. Here’s what I tried: Used listEnsemblArchives() to find the host URL for version 112,…
This post contains the analysis steps used to create a differential gene expression results table generated from RNA-seq counts summarised using nf-core/rnaseq. The comparison was done between two conditions: normal versus (lung) cancer. We will be using {edgeR}, so install it if you haven’t already. if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("edgeR") We will also…
I have been using pnas_expression.txt as a test dataset for count table analyses for many years. It was created by Davis McCarthy and was hosted on their Google Sites website. After some time, the site became unavailable and I have been hosting it on my web server since then. The RNA-seq libraries were generated using…
ARCHS4 (All RNA-seq and ChIP-seq sample and signature search) is a resource that provides access to gene and transcript counts uniformly processed (using kallisto) from all human and mouse RNA-seq experiments from the Gene Expression Omnibus (GEO) and the Sequence Read Archive (SRA). The tool gget and the sub-tool archs4 can be used to query…
Tidy data is a standard way of mapping the meaning of a dataset to its structure. A dataset is messy or tidy depending on how rows, columns and tables are matched up with observations, variables and types. In tidy data: Each variable forms a column. Each observation forms a row. Each type of observational unit…
ffq is a tool that can be used to fetch metadata from several data repositories. It can also be used to generate links to raw data hosted at the EBI (via FTP), AWS, GCP, and NCBI. I wrote a short Bash script called ffs that can generate the commands needed to download the raw data…
I just finished reading "Using prototyping to choose a bioinformatics workflow management system", which I summarised on Mastodon as follows: Enjoyed reading "Using prototyping to choose a #bioinformatics workflow management system". Paper describes authors’ 10 day experience searching and implementing a workflow. Summary: Need to decide which tool to use? Shortlist a list of potentially…
The Pachter Lab have developed some very useful bioinformatics software. In this post, I use gget to quickly query ARCHS4 on the command line to see where a gene of interest is expressed. The gget tool has other functionality too including sequence alignment, enrichment analysis, and even protein structure prediction using AlphaFold. Check it out!…
The Sequence Read Archive (SRA) is the largest publicly available repository of high throughput sequencing data. (Fun fact: it used to be called the Short Read Archive since most of the data was from short read sequencers.) The tool fastq-dump from the SRA Toolkit can be used to download SRA data. A while ago I…