uncoverappLib
This is the released version of uncoverappLib; for the devel version, see uncoverappLib.
Interactive graphical application for clinical assessment of sequence coverage at the base-pair level
Bioconductor version: Release (3.23)
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("uncoverappLib")):
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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, Coverage, Software, Visualization |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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_1.22.0.tar.gz |
| Windows Binary (x86_64) | uncoverappLib_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | uncoverappLib_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | uncoverappLib_1.22.0.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 |