countsimQC
This is the released version of countsimQC; for the devel version, see countsimQC.
Compare Characteristic Features of Count Data Sets
Bioconductor version: Release (3.23)
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("countsimQC")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | ExperimentalDesign, ImmunoOncology, Microbiome, QualityControl, RNASeq, ReportWriting, SingleCell, Software, Visualization |
| Version | 1.30.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 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, rlang |
| System Requirements | |
| URL | https://github.com/csoneson/countsimQC |
| Bug Reports | https://github.com/csoneson/countsimQC/issues |
See More
| Suggests | knitr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | muscat |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | countsimQC_1.30.0.tar.gz |
| Windows Binary (x86_64) | countsimQC_1.30.0.zip |
| macOS Binary (big-sur-x86_64) | countsimQC_1.30.0.tgz |
| macOS Binary (sonoma-arm64) | countsimQC_1.30.0.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 |