countsimQC

DOI: 10.18129/B9.bioc.countsimQC    

This is the development version of countsimQC; for the stable release version, see countsimQC.

Compare Characteristic Features of Count Data Sets

Bioconductor version: Development (3.12)

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 "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.7.2
In Bioconductor since BioC 3.8 (R-3.5) (2 years)
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 https://github.com/csoneson/countsimQC
BugReports 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_1.7.2.tar.gz
Windows Binary countsimQC_1.7.2.zip
macOS 10.13 (High Sierra) countsimQC_1.7.2.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

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