crisprVerse

Collection of R packages that work in harmony for CRISPR gRNA design

https://github.com/crisprverse/crisprverse

Keywords

Keywords from Contributors

Repository

Collection of R packages that work in harmony for CRISPR gRNA design

https://github.com/crisprVerse/crisprVerse/blob/master/

crisprVerse: ecosystem of R packages for CRISPR gRNA design
================

-   Installation and getting
    started
-   Components
-   Reproducibility

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    ## The following packages are out of date: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

Owner

GitHub Events

Committers

Last synced: over 2 years ago

Issues and Pull Requests

Last synced: 6 months ago

Packages