countsimQC

Compare Characteristic Features of Count Data Sets

Bioconductor version: 3.23 · Package version: 1.30.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("countsimQC")

Details

Maintainer	Charlotte Soneson <charlottesoneson@gmail.com>
Author	Charlotte Soneson [aut, cre] (ORCID: <https://orcid.org/0000-0003-3833-2169>)
License	GPL (>=2)
URL	https://github.com/csoneson/countsimQC
Bug Reports	https://github.com/csoneson/countsimQC/issues
Downloads rank	534
Source branch	RELEASE_3_23
biocViews	ExperimentalDesign, ImmunoOncology, Microbiome, QualityControl, RNASeq, ReportWriting, SingleCell, Software, Visualization

Documentation

countsimQC - Comparing characteristic features across count data sets

Download

Source package

Dependencies

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, rlang

Suggests: knitr, testthat

Reverse dependencies

Suggests Me (1): muscat