alevinQC

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

Generate QC Reports For Alevin Output

Bioconductor version: Development (3.24)

Generate QC reports summarizing the output from an alevin, alevin-fry, or simpleaf run. Reports can be generated as html or pdf files, or as shiny applications.

Author: Charlotte Soneson [aut, cre] ORCID: 0000-0003-3833-2169 , Avi Srivastava [aut], Rob Patro [aut], Dongze He [aut]

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

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

Charlotte Soneson, Avi Srivastava, Rob Patro, Dongze He. alevinQC: Generate QC Reports For Alevin Output. doi:10.18129/B9.bioc.alevinQC, R package version 1.29.0, https://bioconductor.org/packages/alevinQC.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("alevinQC")

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("alevinQC")

alevinQC	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	QualityControl, SingleCell, Software
Version	1.29.0
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0)
Imports	rmarkdown (>= 2.5), tools, methods, ggplot2 (>= 3.4.0), GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils, tximport (>= 1.17.4), cowplot, rlang, Rcpp
System Requirements
URL	https://github.com/csoneson/alevinQC
Bug Reports	https://github.com/csoneson/alevinQC/issues

Suggests	knitr, BiocStyle, testthat (>= 3.0.0), BiocManager
Linking To	Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	alevinQC_1.29.0.tar.gz
Windows Binary (x86_64)	alevinQC_1.29.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	alevinQC_1.29.0.tgz
macOS Binary (sonoma-arm64)	alevinQC_1.29.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/alevinQC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/alevinQC
Package Short Url	https://bioconductor.org/packages/alevinQC/
Package Downloads Report	Download Stats