Package: crisprViz 1.7.0

Jean-Philippe Fortin

crisprViz: Visualization Functions for CRISPR gRNAs

Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.

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

crisprViz_1.7.0.tar.gz

crisprViz_1.7.0.tar.gz(r-4.5-noble)crisprViz_1.7.0.tar.gz(r-4.4-noble)
crisprViz_1.7.0.tgz(r-4.4-emscripten)crisprViz_1.7.0.tgz(r-4.3-emscripten)
crisprViz.pdf |crisprViz.html✨
crisprViz/json (API)
NEWS

# Install 'crisprViz' in R:

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

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

Datasets:

cage - CAGE peak annotation from AnnotationHub
cas12aGuideSet - Example GuideSet targeting the human LTN1 gene.
cas9GuideSet - Example GuideSet targeting the human LTN1 gene.
dnase - DNase I hypersensitive site annotation from AnnotationHub
gpr21GeneModel - CompressedGRangesList describing the human GPR21 gene.
gpr21GuideSet - Example GuideSet targeting the human GPR21 gene.
krasGeneModel - CompressedGRangesList describing the human KRAS gene.
krasGuideSet - Example GuideSet targeting the human KRAS gene.
ltn1GeneModel - CompressedGRangesList describing the human LTN1 gene.
mmp7GeneModel - CompressedGRangesList describing the human MMP7 gene.
mmp7GuideSet - Example GuideSet targeting the human MMP7 gene.
repeats - Subset of repeat elements for hg38.

On BioConductor:crisprViz-1.7.0(bioc 3.20)crisprViz-1.6.0(bioc 3.19)

bioconductor-package

2 exports 1.24 score 170 dependencies 2 dependents

Last updated 2 months agofrom:d9192adfb6

Exports:plotGuideSet plotMultipleGuideSets

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 cpp11 crayon crisprBase crisprBowtie crisprDesign crisprScore crisprScoreData curl data.table DBI dbplyr DelayedArray deldir dichromat digest dir.expiry dplyr 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 httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr 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 snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 XVector yaml zlibbioc

Introduction to crisprViz

Luke Hoberecht

Rendered fromintro.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-10-17
Started: 2022-07-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CAGE peak annotation from AnnotationHub	cage
Example GuideSet targeting the human LTN1 gene.	cas12aGuideSet
Example GuideSet targeting the human LTN1 gene.	cas9GuideSet
DNase I hypersensitive site annotation from AnnotationHub	dnase
CompressedGRangesList describing the human GPR21 gene.	gpr21GeneModel
Example GuideSet targeting the human GPR21 gene.	gpr21GuideSet
CompressedGRangesList describing the human KRAS gene.	krasGeneModel
Example GuideSet targeting the human KRAS gene.	krasGuideSet
CompressedGRangesList describing the human LTN1 gene.	ltn1GeneModel
CompressedGRangesList describing the human MMP7 gene.	mmp7GeneModel
Example GuideSet targeting the human MMP7 gene.	mmp7GuideSet
Plotting a GuideSet and other genomic annotations	plotGuideSet
Plotting a GuideSet and other genomic annotation	plotMultipleGuideSets
Subset of repeat elements for hg38.	repeats