Authors: Jean-Philippe Fortin, Luke Hoberecht
Date: July 25, 2022
The crisprVerse is a collection of
packages for CRISPR guide RNA (gRNA) design that can easily be installed
with the crisprVerse package. This provides a convenient way of
downloading and installing all crisprVerse packages with a single R
command.
The package can be installed from the Bioconductor devel branch using the following commands in an R session:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version="devel")
BiocManager::install("crisprVerse")The core crisprVerse includes the packages that are commonly used for
gRNA design, and are attached when you attach the crisprVerse package:
library(crisprVerse)## Warning: multiple methods tables found for 'aperm'
## Warning: replacing previous import 'BiocGenerics::aperm' by
## 'DelayedArray::aperm' when loading 'SummarizedExperiment'
You can check that all crisprVerse packages are up-to-date with
crisprVerse_update():
crisprVerse_update()## The following packages are out of date:
##
## • crisprDesign (0.99.176 -> 0.99.177)
## • crisprScore (1.1.15 -> 1.1.16)
##
## Start a clean R session then run:
## BiocManager::install(c("crisprDesign", "crisprScore"))
The complete documentation for the package can be found here.
The following packages are installed and loaded with the crisprVerse
package:
- crisprBase to specify and manipulate CRISPR nucleases.
- crisprBowtie to perform gRNA spacer sequence alignment with Bowtie.
- crisprScore to annotate gRNAs with on-target and off-target scores.
- crisprDesign
to design and manipulate gRNAs with
GuideSetobjects. - crisprViz to visualize gRNAs.
sessionInfo()## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.7
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] crisprViz_0.99.22 crisprDesign_0.99.176 crisprScore_1.1.15
## [4] crisprScoreData_1.1.3 ExperimentHub_2.5.0 AnnotationHub_3.5.1
## [7] BiocFileCache_2.5.0 dbplyr_2.2.1 BiocGenerics_0.43.4
## [10] crisprBowtie_1.1.1 crisprBase_1.1.8 crisprVerse_0.99.9
## [13] BiocStyle_2.25.0
##
## loaded via a namespace (and not attached):
## [1] backports_1.4.1 Hmisc_4.7-1
## [3] lazyeval_0.2.2 splines_4.2.1
## [5] BiocParallel_1.31.12 GenomeInfoDb_1.33.7
## [7] ggplot2_3.3.6 digest_0.6.29
## [9] ensembldb_2.21.4 htmltools_0.5.3
## [11] fansi_1.0.3 checkmate_2.1.0
## [13] magrittr_2.0.3 memoise_2.0.1
## [15] BSgenome_1.65.2 cluster_2.1.4
## [17] tzdb_0.3.0 Biostrings_2.65.3
## [19] readr_2.1.2 matrixStats_0.62.0
## [21] prettyunits_1.1.1 jpeg_0.1-9
## [23] colorspace_2.0-3 blob_1.2.3
## [25] rappdirs_0.3.3 xfun_0.32
## [27] dplyr_1.0.10 crayon_1.5.1
## [29] RCurl_1.98-1.8 jsonlite_1.8.0
## [31] survival_3.4-0 VariantAnnotation_1.43.3
## [33] glue_1.6.2 gtable_0.3.1
## [35] zlibbioc_1.43.0 XVector_0.37.1
## [37] DelayedArray_0.23.1 scales_1.2.1
## [39] DBI_1.1.3 Rcpp_1.0.9
## [41] htmlTable_2.4.1 xtable_1.8-4
## [43] progress_1.2.2 reticulate_1.26
## [45] foreign_0.8-82 bit_4.0.4
## [47] Formula_1.2-4 stats4_4.2.1
## [49] htmlwidgets_1.5.4 httr_1.4.4
## [51] dir.expiry_1.5.1 RColorBrewer_1.1-3
## [53] ellipsis_0.3.2 pkgconfig_2.0.3
## [55] XML_3.99-0.10 nnet_7.3-17
## [57] Gviz_1.41.1 deldir_1.0-6
## [59] utf8_1.2.2 tidyselect_1.1.2
## [61] rlang_1.0.5 later_1.3.0
## [63] AnnotationDbi_1.59.1 munsell_0.5.0
## [65] BiocVersion_3.16.0 tools_4.2.1
## [67] cachem_1.0.6 cli_3.4.0
## [69] generics_0.1.3 RSQLite_2.2.16
## [71] evaluate_0.16 stringr_1.4.1
## [73] fastmap_1.1.0 yaml_2.3.5
## [75] knitr_1.40 bit64_4.0.5
## [77] purrr_0.3.4 randomForest_4.7-1.1
## [79] AnnotationFilter_1.21.0 KEGGREST_1.37.3
## [81] Rbowtie_1.37.0 mime_0.12
## [83] xml2_1.3.3 biomaRt_2.53.2
## [85] compiler_4.2.1 rstudioapi_0.14
## [87] filelock_1.0.2 curl_4.3.2
## [89] png_0.1-7 interactiveDisplayBase_1.35.0
## [91] tibble_3.1.8 stringi_1.7.8
## [93] basilisk.utils_1.9.3 GenomicFeatures_1.49.6
## [95] lattice_0.20-45 ProtGenerics_1.29.0
## [97] Matrix_1.4-1 vctrs_0.4.1
## [99] pillar_1.8.1 lifecycle_1.0.1
## [101] BiocManager_1.30.18 data.table_1.14.2
## [103] bitops_1.0-7 httpuv_1.6.5
## [105] rtracklayer_1.57.0 GenomicRanges_1.49.1
## [107] R6_2.5.1 BiocIO_1.7.1
## [109] latticeExtra_0.6-30 promises_1.2.0.1
## [111] gridExtra_2.3 IRanges_2.31.2
## [113] codetools_0.2-18 dichromat_2.0-0.1
## [115] assertthat_0.2.1 SummarizedExperiment_1.27.2
## [117] rjson_0.2.21 GenomicAlignments_1.33.1
## [119] Rsamtools_2.13.4 S4Vectors_0.35.3
## [121] GenomeInfoDbData_1.2.8 parallel_4.2.1
## [123] hms_1.1.2 rpart_4.1.16
## [125] grid_4.2.1 basilisk_1.9.6
## [127] rmarkdown_2.16 MatrixGenerics_1.9.1
## [129] biovizBase_1.45.0 Biobase_2.57.1
## [131] shiny_1.7.2 base64enc_0.1-3
## [133] interp_1.1-3 restfulr_0.0.15