countsimQC

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see countsimQC.

Compare Characteristic Features of Count Data Sets

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0003-3833-2169

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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

Documentation

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

browseVignettes("countsimQC")

countsimQC User Guide HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ExperimentalDesign, ImmunoOncology, Microbiome, QualityControl, RNASeq, ReportWriting, SingleCell, Software, Visualization

Version 1.26.0

In Bioconductor since BioC 3.8 (R-3.5) (7 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

System Requirements

URL https://github.com/csoneson/countsimQC

Bug Reports https://github.com/csoneson/countsimQC/issues

Suggests knitr, testthat

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package countsimQC_1.26.0.tar.gz

Windows Binary (x86_64) countsimQC_1.26.0.zip

macOS Binary (x86_64) countsimQC_1.26.0.tgz

macOS Binary (arm64) countsimQC_1.26.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/countsimQC

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/countsimQC

Bioc Package Browser https://code.bioconductor.org/browse/countsimQC/

Package Short Url https://bioconductor.org/packages/countsimQC/

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