uncoverappLib

DOI: 10.18129/B9.bioc.uncoverappLib    

Interactive graphical application for clinical assessment of sequence coverage at the base-pair level

Bioconductor version: Release (3.15)

a Shiny application containing a suite of graphical and statistical tools to support clinical assessment of low coverage regions.It displays three web pages each providing a different analysis module: Coverage analysis, calculate AF by allele frequency app and binomial distribution. uncoverAPP provides a statisticl summary of coverage given target file or genes name.

Author: Emanuela Iovino [cre, aut], Tommaso Pippucci [aut]

Maintainer: Emanuela Iovino <emanuela.iovino at unibo.it>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("uncoverappLib")

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("uncoverappLib")

 

HTML	R Script	uncoverappLib
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Annotation, Coverage, Software, Visualization
Version	1.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 years)
License	MIT + file LICENSE
Depends
Imports	markdown, shiny, shinyjs, shinyBS, shinyWidgets, shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache, rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils, S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, processx, Rsamtools, GenomicRanges
LinkingTo
Suggests	BiocStyle, knitr, testthat, rmarkdown, dplyr
SystemRequirements
Enhances
URL	https://github.com/Manuelaio/uncoverappLib
BugReports	https://github.com/Manuelaio/uncoverappLib/issues
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	uncoverappLib_1.6.0.tar.gz
Windows Binary	uncoverappLib_1.6.0.zip
macOS Binary (x86_64)	uncoverappLib_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/uncoverappLib
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/uncoverappLib
Package Short Url	https://bioconductor.org/packages/uncoverappLib/
Package Downloads Report	Download Stats