This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see countsimQC.
Bioconductor version: 3.16
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")
):
To install this package, start R (version "4.2") 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.
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 |
Reference Manual | ||
Text | NEWS |
biocViews | ExperimentalDesign, ImmunoOncology, Microbiome, QualityControl, RNASeq, ReportWriting, SingleCell, Software, Visualization |
Version | 1.16.1 |
In Bioconductor since | BioC 3.8 (R-3.5) (4.5 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 |
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 |
Follow Installation instructions to use this package in your R session.
Source Package | countsimQC_1.16.1.tar.gz |
Windows Binary | countsimQC_1.16.1.zip |
macOS Binary (x86_64) | countsimQC_1.16.1.tgz |
macOS Binary (arm64) | countsimQC_1.16.1.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 |
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