Computational biology and genomics
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…