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Read RNA-seq Output from nf-core/rnaseq

Source: R/read_rnaseq_out.R
read_rnaseq_out.Rd

This function loads and formats a `SummarizedExperiment` object from the nf-core/rnaseq output directory (e.g., generated using STAR + Salmon). It sets up TPM, log-transformed TPM, cleans the sample annotations, and adds basic QC metadata (number of counts and detected features).

Usage

read_rnaseq_out(DATA_PATH)

Arguments

DATA_PATH

A character string pointing to the path containing nf-core/rnaseq results.

Value

A `SummarizedExperiment` object with assays and annotations formatted.