countsimQC

Compare Characteristic Features of Count Data Sets

Bioconductor version: Release (3.17)

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 gmail.com>

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

Installation

To install this package, start R (version "4.3") 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

Details

biocViews	ExperimentalDesign, ImmunoOncology, Microbiome, QualityControl, RNASeq, ReportWriting, SingleCell, Software, Visualization
Version	1.18.0
In Bioconductor since	BioC 3.8 (R-3.5) (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
Linking To
Suggests	knitr, testthat
System Requirements
Enhances
URL	https://github.com/csoneson/countsimQC
Bug Reports	https://github.com/csoneson/countsimQC/issues

Depends On Me
Imports Me
Suggests Me	muscat
Links To Me
Build Report

Package Archives

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

Source Package	countsimQC_1.18.0.tar.gz
Windows Binary	countsimQC_1.18.0.zip
macOS Binary (x86_64)	countsimQC_1.18.0.tgz
macOS Binary (arm64)	countsimQC_1.18.0.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/
Package Downloads Report	Download Stats