crisprScoreData

• Installation from Bioconductor
• Exploring the different data in crisprScoreData

Authors: Jean-Philippe Fortin

Installation from Bioconductor

crisprScoreData can be installed from the Bioconductor devel branch using the following commands in a fresh R session:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(version="devel")
BiocManager::install("crisprScoreData")

Exploring the different data in crisprScoreData

We first load the crisprScoreData package:

library(crisprScoreData)

## Loading required package: ExperimentHub

## Loading required package: BiocGenerics

## 
## Attaching package: 'BiocGenerics'

## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs

## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, basename, cbind, colnames,
##     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
##     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
##     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
##     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
##     union, unique, unsplit, which.max, which.min

## Loading required package: AnnotationHub

## Loading required package: BiocFileCache

## Loading required package: dbplyr

This package contains several pre-trained models for different on-target activity prediction algorithms to be used in the package crisprScore.

We can access the file paths of the different pre-trained models directly with named functions:

# For DeepHF model:
DeepWt.hdf5()

## snapshotDate(): 2022-08-23

## see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation

## loading from cache

##                                                                             EH6123 
## "/Users/fortinj2/Library/Caches/org.R-project.R/R/ExperimentHub/f2d463daf223_6166"

DeepWt_T7.hdf5()

## snapshotDate(): 2022-08-23

## see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation

## loading from cache

##                                                                             EH6124 
## "/Users/fortinj2/Library/Caches/org.R-project.R/R/ExperimentHub/f2d43b4f0b0c_6167"

DeepWt_U6.hdf5()

## snapshotDate(): 2022-08-23

## see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation

## loading from cache

##                                                                              EH6125 
## "/Users/fortinj2/Library/Caches/org.R-project.R/R/ExperimentHub/1646f4d5dfe8e_6168"

esp_rnn_model.hdf5()

## snapshotDate(): 2022-08-23

## see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation

## loading from cache

##                                                                             EH6126 
## "/Users/fortinj2/Library/Caches/org.R-project.R/R/ExperimentHub/f2d4425e5f3f_6169"

hf_rnn_model.hdf5()

## snapshotDate(): 2022-08-23

## see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation

## loading from cache

##                                                                             EH6127 
## "/Users/fortinj2/Library/Caches/org.R-project.R/R/ExperimentHub/f2d441bf4323_6170"

# For Lindel model:
Model_weights.pkl()

## snapshotDate(): 2022-08-23

## see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation

## loading from cache

##                                                                             EH6128 
## "/Users/fortinj2/Library/Caches/org.R-project.R/R/ExperimentHub/f2d473d0d08d_6171"

Or we can access them using the ExperimentHub interface:

eh <- ExperimentHub()

## snapshotDate(): 2022-08-23

query(eh, "crisprScoreData")

## ExperimentHub with 9 records
## # snapshotDate(): 2022-08-23
## # $dataprovider: Fudan University, UCSF, University of Washington, New York ...
## # $species: NA
## # $rdataclass: character
## # additional mcols(): taxonomyid, genome, description,
## #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## #   rdatapath, sourceurl, sourcetype 
## # retrieve records with, e.g., 'object[["EH6123"]]' 
## 
##            title             
##   EH6123 | DeepWt.hdf5       
##   EH6124 | DeepWt_T7.hdf5    
##   EH6125 | DeepWt_U6.hdf5    
##   EH6126 | esp_rnn_model.hdf5
##   EH6127 | hf_rnn_model.hdf5 
##   EH6128 | Model_weights.pkl 
##   EH7304 | CRISPRa_model.pkl 
##   EH7305 | CRISPRi_model.pkl 
##   EH7356 | RFcombined.rds

eh[["EH6127"]]

## see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation

## loading from cache

##                                                                             EH6127 
## "/Users/fortinj2/Library/Caches/org.R-project.R/R/ExperimentHub/f2d441bf4323_6170"

For details on the source of these files, and on their construction see ?crisprScoreData and the scripts:

• inst/scripts/make-metadata.R
• inst/scripts/make-data.Rmd

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] crisprScoreData_1.1.3 ExperimentHub_2.5.0   AnnotationHub_3.5.0  
## [4] BiocFileCache_2.5.0   dbplyr_2.2.1          BiocGenerics_0.43.1  
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.9                    png_0.1-7                    
##  [3] Biostrings_2.65.2             assertthat_0.2.1             
##  [5] digest_0.6.29                 utf8_1.2.2                   
##  [7] mime_0.12                     R6_2.5.1                     
##  [9] GenomeInfoDb_1.33.5           stats4_4.2.1                 
## [11] RSQLite_2.2.16                evaluate_0.16                
## [13] httr_1.4.4                    pillar_1.8.1                 
## [15] zlibbioc_1.43.0               rlang_1.0.4                  
## [17] curl_4.3.2                    rstudioapi_0.14              
## [19] blob_1.2.3                    S4Vectors_0.35.1             
## [21] rmarkdown_2.15.2              stringr_1.4.1                
## [23] RCurl_1.98-1.8                bit_4.0.4                    
## [25] shiny_1.7.2                   compiler_4.2.1               
## [27] httpuv_1.6.5                  xfun_0.32                    
## [29] pkgconfig_2.0.3               htmltools_0.5.3              
## [31] tidyselect_1.1.2              KEGGREST_1.37.3              
## [33] tibble_3.1.8                  GenomeInfoDbData_1.2.8       
## [35] interactiveDisplayBase_1.35.0 IRanges_2.31.2               
## [37] fansi_1.0.3                   crayon_1.5.1                 
## [39] dplyr_1.0.9                   later_1.3.0                  
## [41] bitops_1.0-7                  rappdirs_0.3.3               
## [43] xtable_1.8-4                  lifecycle_1.0.1              
## [45] DBI_1.1.3                     magrittr_2.0.3               
## [47] cli_3.3.0                     stringi_1.7.8                
## [49] cachem_1.0.6                  XVector_0.37.0               
## [51] promises_1.2.0.1              ellipsis_0.3.2               
## [53] filelock_1.0.2                generics_0.1.3               
## [55] vctrs_0.4.1                   tools_4.2.1                  
## [57] bit64_4.0.5                   Biobase_2.57.1               
## [59] glue_1.6.2                    purrr_0.3.4                  
## [61] BiocVersion_3.16.0            fastmap_1.1.0                
## [63] yaml_2.3.5                    AnnotationDbi_1.59.1         
## [65] BiocManager_1.30.18           memoise_2.0.1                
## [67] knitr_1.40