alevinQC

The alevinQC R package provides functionality for generating QC reports summarizing the output of alevin (Srivastava et al., Genome Biology 20:65 (2019)). The reports can be generated in html or pdf format, or as R/Shiny applications.

Installation:

alevinQC is available from Bioconductor, and can be installed using the BiocManager CRAN package:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("alevinQC")

Note that alevinQC v 1.1 or newer is required to process output from Salmon version 0.14.0 or newer.

Example usage:

alevinQCReport(baseDir = system.file("extdata/alevin_example_v0.14", 
                                     package = "alevinQC"),
               sampleId = "testSample", 
               outputFile = "alevinReport.html", 
               outputFormat = "html_document",
               outputDir = tempdir(), forceOverwrite = TRUE)

For more information, we refer to the package vignette.