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Compare Characteristic Features of Count Data Sets

Bioconductor version: Release (3.19)

countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.

Author: Charlotte Soneson [aut, cre]

Maintainer: Charlotte Soneson <charlottesoneson at>

Citation (from within R, enter citation("countsimQC")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

countsimQC User Guide HTML R Script
Reference Manual PDF


biocViews ExperimentalDesign, ImmunoOncology, Microbiome, QualityControl, RNASeq, ReportWriting, SingleCell, Software, Visualization
Version 1.22.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL (>=2)
Depends R (>= 3.5)
Imports rmarkdown (>= 2.5), edgeR, DESeq2(>= 1.16.0), dplyr, tidyr, ggplot2, grDevices, tools, SummarizedExperiment, genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods, ragg
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Follow Installation instructions to use this package in your R session.

Source Package countsimQC_1.22.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) countsimQC_1.22.0.tgz
macOS Binary (arm64) countsimQC_1.22.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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