crisprVerse: ecosystem of R packages for CRISPR gRNA design ================ - <a href="#installation-and-getting-started" id="toc-installation-and-getting-started">Installation and getting started</a> - <a href="#components" id="toc-components">Components</a> - <a href="#reproducibility" id="toc-reproducibility">Reproducibility</a> Authors: Jean-Philippe Fortin, Luke Hoberecht Date: July 25, 2022 # Installation and getting started The [crisprVerse](https://github.com/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: ``` r 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: ``` r 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packages are up-to-date with `crisprVerse_update()`: ``` r crisprVerse_update() ``` ## The following packages are out of date: ## ## • crisprDesign (0.99.176 -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](https://bioconductor.org/packages/devel/bioc/manuals/crisprVerse/man/crisprVerse.pdf). # Components The following packages are installed and loaded with the `crisprVerse` package: - *[crisprBase](https://bioconductor.org/packages/3.16/crisprBase)* to specify and manipulate CRISPR nucleases. - *[crisprBowtie](https://bioconductor.org/packages/3.16/crisprBowtie)* to perform gRNA spacer sequence alignment with Bowtie. - *[crisprScore](https://bioconductor.org/packages/3.16/crisprScore)* to annotate gRNAs with on-target and off-target scores. - *[crisprDesign](https://bioconductor.org/packages/3.16/crisprDesign)* to design and manipulate gRNAs with `GuideSet` objects. - *[crisprViz](https://bioconductor.org/packages/3.16/crisprViz)* to visualize gRNAs. # Reproducibility ``` r 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