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uncoverappLib

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

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


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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

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")
uncoverappLib HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Annotation, Coverage, Software, Visualization
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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, processx, Rsamtools, GenomicRanges
System Requirements
URL https://github.com/Manuelaio/uncoverappLib
Bug Reports https://github.com/Manuelaio/uncoverappLib/issues
See More
Suggests BiocStyle, knitr, testthat, rmarkdown, dplyr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package uncoverappLib_1.13.0.tar.gz
Windows Binary uncoverappLib_1.13.0.zip
macOS Binary (x86_64) uncoverappLib_1.13.0.tgz
macOS Binary (arm64) uncoverappLib_1.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/uncoverappLib
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/uncoverappLib
Bioc Package Browser https://code.bioconductor.org/browse/uncoverappLib/
Package Short Url https://bioconductor.org/packages/uncoverappLib/
Package Downloads Report Download Stats