Computational biology and genomics
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…
It has been 14 years since I’ve started this blog and as per tradition, I write a blog post reflecting on stuff. It’s a loose tradition since some years I didn’t write anything. When I do write, it’s usually about something new I’ve learned and/or started practising since the last anniversary post. Recently, I’ve been…
There’s this nice tip from a book I had read a long time ago. Some of the tips/lessons from the aforementioned book weren’t useful to me but the following tip is something that I have found quite effective in getting stuff done. Say you have some task to do and you’re finding it hard to…
I came across this question last night on some trivia app I have on my phone: When you let fruits consisting of 99% water by weight dry so that they become 98% water, what percentage of weight do they lose? Stop scrolling (or looking) down right now, if you want to give it some thought…
When you use remotes::install_github() too often in a short span of time, GitHub may rate limit you. This means you can’t use install the package you wanted without waiting for the rate limit to end. One way around this (and to prevent getting rate limited) is to simply clone the repo and use remotes::install_local()! To…
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…
Today I learned of the utils::getAnywhere() function in R, which I discovered when looking for a way to determine which function is going to be used when two attached packages have the same function name. I knew of base::search() which provides the search path used by R to look for objects (remember that everything in…
If you find yourself getting a "Timeout of 60 seconds was reached" warning from download.file that’s preventing you from installing a package, you can increase the timeout in R by using options(). For example, when I was trying to run the following command: SeuratData::InstallData('ifnb') trying URL 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz' Content type 'application/octet-stream' length 413266233 bytes (394.1 MB)…