diff --git a/DESCRIPTION b/DESCRIPTION
index 84387ce..3cac73d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: crisprScore
-Version: 1.1.16
-Date: 2022-10-22
+Version: 1.1.17
+Date: 2022-10-17
Title: On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
Authors@R: c(
person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre", "cph")),
diff --git a/README.Rmd b/README.Rmd
index 6d083e3..7eaab45 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -10,24 +10,26 @@ bibliography: vignettes/references.bib
options("knitr.graphics.auto_pdf"=TRUE)
```
-Authors: Jean-Philippe Fortin, Aaron Lun, Luke Hoberecht
+Authors: Jean-Philippe Fortin, Aaron Lun, Luke Hoberecht, Pirunthan Perampalan
Date: July 1, 2022
# Overview
-crisprScore provides R wrappers of several on-target and off-target scoring
+The `crisprScore` package provides R wrappers of several on-target and off-target scoring
methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported:
SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target
cutting efficiency scoring methods are RuleSet1, RuleSet3, Azimuth, DeepHF,
-DeepSpCas9, DeepCpf1, enPAM+GB, CRISPRscan and CRISPRater. Both the CFD and MIT
+DeepSpCas9, DeepCpf1, enPAM+GB, CRISPRscan and CRISPRater. Both the CFD and MIT
scoring methods are available for off-target specificity prediction. The
package also provides a Lindel-derived score to predict the probability
of a gRNA to produce indels inducing a frameshift for the Cas9 nuclease.
Note that DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines.
Our work is described in a recent bioRxiv preprint:
-["A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies"](https://www.biorxiv.org/content/10.1101/2022.04.21.488824v2)
+["The crisprVerse: A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies"](https://www.biorxiv.org/content/10.1101/2022.04.21.488824v3)
+
+Our main gRNA design package [crisprDesign](https://github.com/crisprVerse/crisprDesign) utilizes the `crisprScore` package to add on- and off-target scores to user-designed gRNAs; check out our [Cas9 gRNA tutorial page](https://github.com/crisprVerse/Tutorials/tree/master/Design_CRISPRko_Cas9) to learn how to use `crisprScore` via `crisprDesign`.
# Installation and getting started
diff --git a/README.md b/README.md
index 4e725a9..d9cbe78 100644
--- a/README.md
+++ b/README.md
@@ -43,27 +43,35 @@ crisprScore: on-target and off-target scoring for CRISPR gRNAs
- Reproducibility
- References
-Authors: Jean-Philippe Fortin, Aaron Lun, Luke Hoberecht
+Authors: Jean-Philippe Fortin, Aaron Lun, Luke Hoberecht, Pirunthan
+Perampalan
Date: July 1, 2022
# Overview
-crisprScore provides R wrappers of several on-target and off-target
-scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases
-are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The
-available on-target cutting efficiency scoring methods are RuleSet1,
-RuleSet3, Azimuth, DeepHF, DeepSpCas9, DeepCpf1, enPAM+GB, CRISPRscan
-and CRISPRater. Both the CFD and MIT scoring methods are available for
-off-target specificity prediction. The package also provides a
-Lindel-derived score to predict the probability of a gRNA to produce
-indels inducing a frameshift for the Cas9 nuclease. Note that DeepHF,
-DeepCpf1 and enPAM+GB are not available on Windows machines.
-
-Our work is described in a recent bioRxiv preprint: [“A comprehensive
-Bioconductor ecosystem for the design of CRISPR guide RNAs across
-nucleases and
-technologies”](https://www.biorxiv.org/content/10.1101/2022.04.21.488824v2)
+The `crisprScore` package provides R wrappers of several on-target and
+off-target scoring methods for CRISPR guide RNAs (gRNAs). The following
+nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d
+(CasRx). The available on-target cutting efficiency scoring methods are
+RuleSet1, RuleSet3, Azimuth, DeepHF, DeepSpCas9, DeepCpf1, enPAM+GB,
+CRISPRscan and CRISPRater. Both the CFD and MIT scoring methods are
+available for off-target specificity prediction. The package also
+provides a Lindel-derived score to predict the probability of a gRNA to
+produce indels inducing a frameshift for the Cas9 nuclease. Note that
+DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines.
+
+Our work is described in a recent bioRxiv preprint: [“The crisprVerse: A
+comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs
+across nucleases and
+technologies”](https://www.biorxiv.org/content/10.1101/2022.04.21.488824v3)
+
+Our main gRNA design package
+[crisprDesign](https://github.com/crisprVerse/crisprDesign) utilizes the
+`crisprScore` package to add on- and off-target scores to user-designed
+gRNAs; check out our [Cas9 gRNA tutorial
+page](https://github.com/crisprVerse/Tutorials/tree/master/Design_CRISPRko_Cas9)
+to learn how to use `crisprScore` via `crisprDesign`.
# Installation and getting started
@@ -643,25 +651,25 @@ sessionInfo()
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
- ## [1] crisprScore_1.1.14 crisprScoreData_1.1.3 ExperimentHub_2.5.0
- ## [4] AnnotationHub_3.5.0 BiocFileCache_2.5.0 dbplyr_2.2.1
- ## [7] BiocGenerics_0.43.1
+ ## [1] crisprScore_1.1.15 crisprScoreData_1.1.3 ExperimentHub_2.5.0
+ ## [4] AnnotationHub_3.5.1 BiocFileCache_2.5.0 dbplyr_2.2.1
+ ## [7] BiocGenerics_0.43.4
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.9 lattice_0.20-45
- ## [3] dir.expiry_1.5.0 png_0.1-7
- ## [5] Biostrings_2.65.2 assertthat_0.2.1
+ ## [3] dir.expiry_1.5.1 png_0.1-7
+ ## [5] Biostrings_2.65.3 assertthat_0.2.1
## [7] digest_0.6.29 utf8_1.2.2
## [9] mime_0.12 R6_2.5.1
- ## [11] GenomeInfoDb_1.33.5 stats4_4.2.1
+ ## [11] GenomeInfoDb_1.33.7 stats4_4.2.1
## [13] RSQLite_2.2.16 evaluate_0.16
## [15] highr_0.9 httr_1.4.4
- ## [17] pillar_1.8.1 basilisk_1.9.3
- ## [19] zlibbioc_1.43.0 rlang_1.0.4
+ ## [17] pillar_1.8.1 basilisk_1.9.6
+ ## [19] zlibbioc_1.43.0 rlang_1.0.5
## [21] curl_4.3.2 rstudioapi_0.14
- ## [23] blob_1.2.3 S4Vectors_0.35.1
- ## [25] Matrix_1.4-1 reticulate_1.25
- ## [27] rmarkdown_2.15.2 stringr_1.4.1
+ ## [23] blob_1.2.3 S4Vectors_0.35.3
+ ## [25] Matrix_1.4-1 reticulate_1.26
+ ## [27] rmarkdown_2.16 stringr_1.4.1
## [29] RCurl_1.98-1.8 bit_4.0.4
## [31] shiny_1.7.2 compiler_4.2.1
## [33] httpuv_1.6.5 xfun_0.32
@@ -670,14 +678,14 @@ sessionInfo()
## [39] tibble_3.1.8 GenomeInfoDbData_1.2.8
## [41] interactiveDisplayBase_1.35.0 IRanges_2.31.2
## [43] randomForest_4.7-1.1 fansi_1.0.3
- ## [45] crayon_1.5.1 dplyr_1.0.9
- ## [47] later_1.3.0 basilisk.utils_1.9.1
+ ## [45] crayon_1.5.1 dplyr_1.0.10
+ ## [47] later_1.3.0 basilisk.utils_1.9.3
## [49] bitops_1.0-7 rappdirs_0.3.3
## [51] grid_4.2.1 jsonlite_1.8.0
## [53] xtable_1.8-4 lifecycle_1.0.1
## [55] DBI_1.1.3 magrittr_2.0.3
- ## [57] cli_3.3.0 stringi_1.7.8
- ## [59] cachem_1.0.6 XVector_0.37.0
+ ## [57] cli_3.4.0 stringi_1.7.8
+ ## [59] cachem_1.0.6 XVector_0.37.1
## [61] promises_1.2.0.1 ellipsis_0.3.2
## [63] filelock_1.0.2 generics_0.1.3
## [65] vctrs_0.4.1 tools_4.2.1
diff --git a/vignettes/crisprScore.Rmd b/vignettes/crisprScore.Rmd
index c88f0ab..5144a1c 100644
--- a/vignettes/crisprScore.Rmd
+++ b/vignettes/crisprScore.Rmd
@@ -29,19 +29,20 @@ options("knitr.graphics.auto_pdf"=TRUE)
# Overview
-crisprScore provides R wrappers of several on-target and off-target scoring
+The `crisprScore` package provides R wrappers of several on-target and off-target scoring
methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported:
SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target
cutting efficiency scoring methods are RuleSet1, RuleSet3, Azimuth, DeepHF,
-DeepSpCas9, DeepCpf1, enPAM+GB, CRISPRscan and CRISPRater. Both the CFD and MIT
+DeepSpCas9, DeepCpf1, enPAM+GB, CRISPRscan and CRISPRater. Both the CFD and MIT
scoring methods are available for off-target specificity prediction. The
package also provides a Lindel-derived score to predict the probability
of a gRNA to produce indels inducing a frameshift for the Cas9 nuclease.
Note that DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines.
Our work is described in a recent bioRxiv preprint:
-["A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies"](https://www.biorxiv.org/content/10.1101/2022.04.21.488824v2)
+["The crisprVerse: A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies"](https://www.biorxiv.org/content/10.1101/2022.04.21.488824v3)
+Our main gRNA design package [crisprDesign](https://github.com/crisprVerse/crisprDesign) utilizes the `crisprScore` package to add on- and off-target scores to user-designed gRNAs; check out our [Cas9 gRNA tutorial page](https://github.com/crisprVerse/Tutorials/tree/master/Design_CRISPRko_Cas9) to learn how to use `crisprScore` via `crisprDesign`.
# Installation and getting started