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:
You can check that all crisprVerse packages are up-to-date with the
function crisprVerse_update().
The following packages are installed and loaded with the
crisprVerse package:
GuideSet objects.## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] crisprViz_1.9.0 crisprDesign_1.9.0 crisprScore_1.11.0
## [4] crisprScoreData_1.10.0 ExperimentHub_2.15.0 AnnotationHub_3.15.0
## [7] BiocFileCache_2.15.1 dbplyr_2.5.0 BiocGenerics_0.53.6
## [10] generics_0.1.3 crisprBowtie_1.11.0 crisprBase_1.11.0
## [13] crisprVerse_1.9.0 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.17.1
## [3] sys_3.4.3 jsonlite_1.8.9
## [5] magrittr_2.0.3 GenomicFeatures_1.59.1
## [7] rmarkdown_2.29 BiocIO_1.17.1
## [9] vctrs_0.6.5 memoise_2.0.1
## [11] Rsamtools_2.23.1 RCurl_1.98-1.16
## [13] base64enc_0.1-3 htmltools_0.5.8.1
## [15] S4Arrays_1.7.3 progress_1.2.3
## [17] curl_6.2.0 SparseArray_1.7.5
## [19] Formula_1.2-5 sass_0.4.9
## [21] bslib_0.9.0 htmlwidgets_1.6.4
## [23] basilisk_1.19.1 Gviz_1.51.0
## [25] httr2_1.1.0 cachem_1.1.0
## [27] buildtools_1.0.0 GenomicAlignments_1.43.0
## [29] lifecycle_1.0.4 pkgconfig_2.0.3
## [31] Matrix_1.7-2 R6_2.6.1
## [33] fastmap_1.2.0 GenomeInfoDbData_1.2.13
## [35] MatrixGenerics_1.19.1 digest_0.6.37
## [37] colorspace_2.1-1 AnnotationDbi_1.69.0
## [39] S4Vectors_0.45.4 Hmisc_5.2-2
## [41] GenomicRanges_1.59.1 RSQLite_2.3.9
## [43] filelock_1.0.3 randomForest_4.7-1.2
## [45] httr_1.4.7 abind_1.4-8
## [47] compiler_4.4.2 Rbowtie_1.47.0
## [49] bit64_4.6.0-1 backports_1.5.0
## [51] htmlTable_2.4.3 BiocParallel_1.41.1
## [53] DBI_1.2.3 biomaRt_2.63.1
## [55] rappdirs_0.3.3 DelayedArray_0.33.6
## [57] rjson_0.2.23 tools_4.4.2
## [59] foreign_0.8-88 nnet_7.3-20
## [61] glue_1.8.0 restfulr_0.0.15
## [63] grid_4.4.2 checkmate_2.3.2
## [65] cluster_2.1.8 gtable_0.3.6
## [67] BSgenome_1.75.1 tzdb_0.4.0
## [69] ensembldb_2.31.0 data.table_1.16.4
## [71] hms_1.1.3 xml2_1.3.6
## [73] XVector_0.47.2 BiocVersion_3.21.1
## [75] pillar_1.10.1 stringr_1.5.1
## [77] dplyr_1.1.4 lattice_0.22-6
## [79] deldir_2.0-4 rtracklayer_1.67.0
## [81] bit_4.5.0.1 biovizBase_1.55.0
## [83] tidyselect_1.2.1 maketools_1.3.2
## [85] Biostrings_2.75.3 knitr_1.49
## [87] gridExtra_2.3 ProtGenerics_1.39.2
## [89] IRanges_2.41.3 SummarizedExperiment_1.37.0
## [91] stats4_4.4.2 xfun_0.50
## [93] Biobase_2.67.0 matrixStats_1.5.0
## [95] stringi_1.8.4 UCSC.utils_1.3.1
## [97] lazyeval_0.2.2 yaml_2.3.10
## [99] evaluate_1.0.3 codetools_0.2-20
## [101] interp_1.1-6 tibble_3.2.1
## [103] BiocManager_1.30.25 cli_3.6.4
## [105] rpart_4.1.24 reticulate_1.40.0
## [107] munsell_0.5.1 jquerylib_0.1.4
## [109] dichromat_2.0-0.1 Rcpp_1.0.14
## [111] GenomeInfoDb_1.43.4 dir.expiry_1.15.0
## [113] png_0.1-8 XML_3.99-0.18
## [115] parallel_4.4.2 ggplot2_3.5.1
## [117] readr_2.1.5 blob_1.2.4
## [119] basilisk.utils_1.19.1 prettyunits_1.2.0
## [121] jpeg_0.1-10 latticeExtra_0.6-30
## [123] AnnotationFilter_1.31.0 bitops_1.0-9
## [125] txdbmaker_1.3.1 VariantAnnotation_1.53.1
## [127] scales_1.3.0 crayon_1.5.3
## [129] rlang_1.1.5 KEGGREST_1.47.0