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.
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.
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.
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