Package: crisprShiny 1.1.0

Jean-Philippe Fortin

crisprShiny: Exploring curated CRISPR gRNAs via Shiny

Provides means to interactively visualize guide RNAs (gRNAs) in GuideSet objects via Shiny application. This GUI can be self-contained or as a module within a larger Shiny app. The content of the app reflects the annotations present in the passed GuideSet object, and includes intuitive tools to examine, filter, and export gRNAs, thereby making gRNA design more user-friendly.

Authors:Jean-Philippe Fortin [aut, cre], Luke Hoberecht [aut]

crisprShiny_1.1.0.tar.gz

crisprShiny_1.1.0.tar.gz(r-4.5-noble)crisprShiny_1.1.0.tar.gz(r-4.4-noble)
crisprShiny_1.1.0.tgz(r-4.4-emscripten)crisprShiny_1.1.0.tgz(r-4.3-emscripten)
crisprShiny.pdf |crisprShiny.html✨
crisprShiny/json (API)
NEWS

# Install 'crisprShiny' in R:

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

Bug tracker:https://github.com/crisprverse/crisprshiny/issues

Datasets:

guideSetExample_basic - Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS
guideSetExample_kras - Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS
guideSetExample_kras_be - Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS
guideSetExample_ntcs - Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS and NTCs
tooltipAnnotation - List of tooltip annotations
tss_kras - Example of a 'GenomicRanges' object storing annotated TSS ranges for the human gene KRAS
txdb_kras - Example of a 'CompressedGenomicRangesList' object storing annotated ranges for the human gene KRAS

On BioConductor:crisprShiny-1.1.0(bioc 3.20)crisprShiny-1.0.0(bioc 3.19)

bioconductor-package

3 exports 1.00 score 184 dependencies

Last updated 2 months agofrom:90d8860815

Exports:crisprServer crisprShiny crisprUI

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass backports base64enc basilisk basilisk.utils BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli clipr cluster codetools colorspace commonmark cpp11 crayon crisprBase crisprBowtie crisprDesign crisprScore crisprScoreData crisprViz crosstalk curl data.table DBI dbplyr DelayedArray deldir dichromat digest dir.expiry dplyr DT ensembldb evaluate ExperimentHub fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable Gviz here highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png prettyunits progress promises ProtGenerics purrr pwalign R6 randomForest rappdirs Rbowtie RColorBrewer Rcpp RcppEigen RcppTOML RCurl readr restfulr reticulate Rhtslib rjson rlang rmarkdown rpart rprojroot Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales shiny shinyBS shinyjs snow sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom waiter withr xfun XML xml2 xtable XVector yaml zlibbioc

Introduction to crisprShiny

Luke Hoberecht, Jean-Philippe Fortin

Rendered fromintro.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2023-10-19
Started: 2023-07-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Server component for crisprShiny App	crisprServer
Interactive visualization of GuideSets via Shiny applications	crisprShiny
UI component for crisprShiny App	crisprUI
Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS	guideSetExample_basic
Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS	guideSetExample_kras
Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS	guideSetExample_kras_be
Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS and NTCs	guideSetExample_ntcs
List of tooltip annotations	tooltipAnnotation
Example of a 'GenomicRanges' object storing annotated TSS ranges for the human gene KRAS	tss_kras
Example of a 'CompressedGenomicRangesList' object storing annotated ranges for the human gene KRAS	txdb_kras