Package: uncoverappLib 1.15.0

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_1.15.0.tar.gz
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uncoverappLib.pdf |uncoverappLib.html✨
uncoverappLib/json (API)
NEWS

# 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-1.15.0(bioc 3.20)uncoverappLib-1.14.0(bioc 3.19)

bioconductor-package

4 exports 0.49 score 180 dependencies

Last updated 2 months agofrom:5881aab674

Exports:buildInput getAnnotationFiles run.uncoverapp uncoverAPP

Dependencies:abind AnnotationDbi AnnotationFilter anytime askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate 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 fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData 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 magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl openxlsx org.Hs.eg.db OrganismDbi pillar pkgconfig plogr 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 sass scales 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 txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 xtable XVector yaml zip zlibbioc

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

Emanuela Iovino , Tommaso Pippucci

Rendered fromuncoverappLib.Rmdusingknitr::rmarkdownon Jun 11 2024.

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