Package: uncoverappLib 1.23.0

Emanuela Iovino

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

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.

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

uncoverappLib_1.23.0.tar.gz
uncoverappLib_1.23.0.zip(r-4.7)uncoverappLib_1.23.0.zip(r-4.6)uncoverappLib_1.23.0.zip(r-4.5)
uncoverappLib_1.23.0.tgz(r-4.6-any)uncoverappLib_1.23.0.tgz(r-4.5-any)
uncoverappLib_1.23.0.tar.gz(r-4.7-any)uncoverappLib_1.23.0.tar.gz(r-4.6-any)
uncoverappLib_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
uncoverappLib/json (API)

# Install 'uncoverappLib' in R:

install.packages('uncoverappLib', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/manuelaio/uncoverapplib/issues

On BioConductor:uncoverappLib-1.23.0(bioc 3.24)uncoverappLib-1.22.0(bioc 3.23)

software visualization annotation coverage

4.59 score 3 stars 13 scripts 4 exports 176 dependencies

Last updated from:720fc62ecd. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	437
linux-devel-x86_64	NOTE	756
source / vignettes	OK	587
linux-release-x86_64	NOTE	738
macos-release-arm64	NOTE	393
macos-oldrel-arm64	NOTE	353
windows-devel	NOTE	546
windows-release	NOTE	532
windows-oldrel	NOTE	525
wasm-release	OK	408

Exports:buildInput getAnnotationFiles run.uncoverapp uncoverAPP

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster codetools colorspace commonmark condformat cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr DT EnsDb.Hsapiens.v75 EnsDb.Hsapiens.v86 ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue GO.db graph gridExtra gtable Gviz highr Hmisc hms Homo.sapiens htmlTable htmltools htmlwidgets httpuv httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle litedown magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mime nnet openssl openxlsx org.Hs.eg.db OrganismDbi otel pillar pkgconfig png prettyunits processx progress promises ProtGenerics ps purrr R6 rappdirs RBGL RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rlist rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo shiny shinyBS shinycssloaders shinyjs shinyWidgets snow sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 xtable XVector yaml zip

uncoverappLib: a R shiny package containing unCOVERApp an interactive graphical application for clinical assessment of sequence coverage at the base-pair level

Introduction | Installation and example | Input file | Output | Session information

Rendered fromuncoverappLib.Rmdusingknitr::rmarkdown

Last update: 2022-10-31
Started: 2020-05-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
wrapper function for getting BiocFileCache associated with uncoverapp package wrapper function for getting BiocFileCache associated with uncoverapp package	.get_cache
Build input file	buildInput
download and rename sorted.bed.gz and sorted.bed.gz.tbi files for annotation of low-coverage positions.	getAnnotationFiles
Location for uncoverapp in RStudio enviroment	run.uncoverapp
run.uncoverapp	uncoverAPP
uncoverappLib: Interactive graphical application for clinical assessment of sequence coverage at the base-pair level	uncoverappLib-package uncoverappLib