countsimQC

DOI: 10.18129/B9.bioc.countsimQC    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see countsimQC.

Compare Characteristic Features of Count Data Sets

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	countsimQC User Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	ExperimentalDesign, ImmunoOncology, Microbiome, QualityControl, RNASeq, ReportWriting, SingleCell, Software, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	GPL (>=2)
Depends	R (>= 3.5)
Imports	rmarkdown (>= 0.9.5), edgeR, DESeq2(>= 1.16.0), dplyr, tidyr, ggplot2, grDevices, tools, SummarizedExperiment, genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods
LinkingTo
Suggests	knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	countsimQC_1.2.0.tar.gz
Windows Binary	countsimQC_1.2.0.zip
Mac OS X 10.11 (El Capitan)	countsimQC_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/countsimQC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/countsimQC
Package Short Url	https://bioconductor.org/packages/countsimQC/
Package Downloads Report	Download Stats