From a5a81393adbb2307bec6a83ce3d79ffa49ceb71f Mon Sep 17 00:00:00 2001 From: Jean-Philippe Fortin Date: Mon, 17 Oct 2022 12:01:24 -0700 Subject: [PATCH] Updated vignette --- DESCRIPTION | 2 +- README.Rmd | 12 ++++++++-- README.md | 56 ++++++++++++++++++++++++--------------------- vignettes/intro.Rmd | 11 +++++---- 4 files changed, 47 insertions(+), 34 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 968ee16..099365a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: crisprViz Title: Visualization Functions for CRISPR gRNAs -Version: 0.99.22 +Version: 0.99.23 Authors@R: c( person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre")), person("Luke", "Hoberecht", email = "lukehob3@gmail.com", role = c("aut")) diff --git a/README.Rmd b/README.Rmd index ccb1f5b..cb8c0f7 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,9 +17,17 @@ knitr::opts_chunk$set(message=FALSE, warning=FALSE) # Introduction -The `crisprViz` package enables the graphical interpretation of `GuideSet` objects from the `crisprDesign` package by plotting guide RNA (gRNA) cutting locations against their target gene or other genomic region. These genomic plots are constructed using the `Gviz` package from Bioconductor. +The `crisprViz` package enables the graphical interpretation of `GuideSet` +objects from the [crisprDesign](https://github.com/crisprVerse/crisprDesign) package by plotting guide RNA (gRNA) +cutting locations against their target gene or other genomic region. + +This vignette walks through several use cases that demonstrate the range of +and how to use plotting functions in the `crisprViz` package. This vignette +also uses our core gRNA design package [crisprDesign](https://github.com/crisprVerse/crisprDesign)to manipulate `GuideSet` objects in +conjunction with plotting in the process of gRNA design. + +Visit our [crisprVerse tutorial page](https://github.com/crisprVerse/Tutorials) to learn more about how to design gRNAs for different applications. -This vignette walks through several use cases that demonstrate the range of and how to use plotting functions in the `crisprViz` package. This vignette also makes heavy use of the `crisprDesign` package to manipulate `GuideSet` objects in conjunction with plotting in the process of gRNA design. For more information about the `crisprDesign` package see [vignettes]. # Installation and getting started diff --git a/README.md b/README.md index fb2f58a..18df5dc 100644 --- a/README.md +++ b/README.md @@ -35,17 +35,21 @@ Date: July 24, 2022 # Introduction The `crisprViz` package enables the graphical interpretation of -`GuideSet` objects from the `crisprDesign` package by plotting guide RNA -(gRNA) cutting locations against their target gene or other genomic -region. These genomic plots are constructed using the `Gviz` package -from Bioconductor. +`GuideSet` objects from the +[crisprDesign](https://github.com/crisprVerse/crisprDesign) package by +plotting guide RNA (gRNA) cutting locations against their target gene or +other genomic region. This vignette walks through several use cases that demonstrate the range of and how to use plotting functions in the `crisprViz` package. This -vignette also makes heavy use of the `crisprDesign` package to -manipulate `GuideSet` objects in conjunction with plotting in the -process of gRNA design. For more information about the `crisprDesign` -package see \[vignettes\]. +vignette also uses our core gRNA design package +[crisprDesign](https://github.com/crisprVerse/crisprDesign)to manipulate +`GuideSet` objects in conjunction with plotting in the process of gRNA +design. + +Visit our [crisprVerse tutorial +page](https://github.com/crisprVerse/Tutorials) to learn more about how +to design gRNAs for different applications. # Installation and getting started @@ -492,20 +496,20 @@ sessionInfo() ## [8] base ## ## other attached packages: - ## [1] crisprViz_0.99.18 crisprDesign_0.99.134 - ## [3] crisprBase_1.1.5 BSgenome.Hsapiens.UCSC.hg38_1.4.4 + ## [1] crisprViz_0.99.22 crisprDesign_0.99.176 + ## [3] crisprBase_1.1.8 BSgenome.Hsapiens.UCSC.hg38_1.4.4 ## [5] BSgenome_1.65.2 rtracklayer_1.57.0 - ## [7] Biostrings_2.65.2 XVector_0.37.0 - ## [9] GenomicRanges_1.49.1 GenomeInfoDb_1.33.5 - ## [11] IRanges_2.31.2 S4Vectors_0.35.1 - ## [13] BiocGenerics_0.43.1 + ## [7] Biostrings_2.65.3 XVector_0.37.1 + ## [9] GenomicRanges_1.49.1 GenomeInfoDb_1.33.7 + ## [11] IRanges_2.31.2 S4Vectors_0.35.3 + ## [13] BiocGenerics_0.43.4 ## ## loaded via a namespace (and not attached): ## [1] backports_1.4.1 Hmisc_4.7-1 - ## [3] AnnotationHub_3.5.0 BiocFileCache_2.5.0 + ## [3] AnnotationHub_3.5.1 BiocFileCache_2.5.0 ## [5] lazyeval_0.2.2 splines_4.2.1 ## [7] BiocParallel_1.31.12 ggplot2_3.3.6 - ## [9] digest_0.6.29 ensembldb_2.21.3 + ## [9] digest_0.6.29 ensembldb_2.21.4 ## [11] htmltools_0.5.3 fansi_1.0.3 ## [13] checkmate_2.1.0 magrittr_2.0.3 ## [15] memoise_2.0.1 cluster_2.1.4 @@ -514,27 +518,27 @@ sessionInfo() ## [21] jpeg_0.1-9 colorspace_2.0-3 ## [23] blob_1.2.3 rappdirs_0.3.3 ## [25] crisprScoreData_1.1.3 xfun_0.32 - ## [27] dplyr_1.0.9 crayon_1.5.1 + ## [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_0.3.0 + ## [33] glue_1.6.2 gtable_0.3.1 ## [35] zlibbioc_1.43.0 DelayedArray_0.23.1 ## [37] scales_1.2.1 DBI_1.1.3 ## [39] Rcpp_1.0.9 htmlTable_2.4.1 ## [41] xtable_1.8-4 progress_1.2.2 - ## [43] reticulate_1.25 foreign_0.8-82 + ## [43] reticulate_1.26 foreign_0.8-82 ## [45] bit_4.0.4 Formula_1.2-4 ## [47] htmlwidgets_1.5.4 httr_1.4.4 - ## [49] dir.expiry_1.5.0 RColorBrewer_1.1-3 + ## [49] dir.expiry_1.5.1 RColorBrewer_1.1-3 ## [51] ellipsis_0.3.2 pkgconfig_2.0.3 ## [53] XML_3.99-0.10 Gviz_1.41.1 ## [55] nnet_7.3-17 dbplyr_2.2.1 ## [57] deldir_1.0-6 utf8_1.2.2 - ## [59] tidyselect_1.1.2 rlang_1.0.4 + ## [59] tidyselect_1.1.2 rlang_1.0.5 ## [61] later_1.3.0 AnnotationDbi_1.59.1 ## [63] munsell_0.5.0 BiocVersion_3.16.0 ## [65] tools_4.2.1 cachem_1.0.6 - ## [67] cli_3.3.0 generics_0.1.3 + ## [67] cli_3.4.0 generics_0.1.3 ## [69] RSQLite_2.2.16 ExperimentHub_2.5.0 ## [71] evaluate_0.16 stringr_1.4.1 ## [73] fastmap_1.1.0 yaml_2.3.5 @@ -547,8 +551,8 @@ sessionInfo() ## [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] crisprScore_1.1.14 highr_0.9 - ## [95] basilisk.utils_1.9.1 GenomicFeatures_1.49.6 + ## [93] crisprScore_1.1.15 highr_0.9 + ## [95] basilisk.utils_1.9.3 GenomicFeatures_1.49.6 ## [97] lattice_0.20-45 ProtGenerics_1.29.0 ## [99] Matrix_1.4-1 vctrs_0.4.1 ## [101] pillar_1.8.1 lifecycle_1.0.1 @@ -558,12 +562,12 @@ sessionInfo() ## [109] latticeExtra_0.6-30 promises_1.2.0.1 ## [111] gridExtra_2.3 codetools_0.2-18 ## [113] dichromat_2.0-0.1 crisprBowtie_1.1.1 - ## [115] assertthat_0.2.1 SummarizedExperiment_1.27.1 + ## [115] assertthat_0.2.1 SummarizedExperiment_1.27.2 ## [117] rjson_0.2.21 GenomicAlignments_1.33.1 ## [119] Rsamtools_2.13.4 GenomeInfoDbData_1.2.8 ## [121] parallel_4.2.1 hms_1.1.2 ## [123] rpart_4.1.16 grid_4.2.1 - ## [125] basilisk_1.9.2 rmarkdown_2.15.2 + ## [125] basilisk_1.9.6 rmarkdown_2.16 ## [127] MatrixGenerics_1.9.1 biovizBase_1.45.0 ## [129] Biobase_2.57.1 shiny_1.7.2 ## [131] base64enc_0.1-3 interp_1.1-3 diff --git a/vignettes/intro.Rmd b/vignettes/intro.Rmd index 0fb1d4c..7b6862f 100644 --- a/vignettes/intro.Rmd +++ b/vignettes/intro.Rmd @@ -24,15 +24,16 @@ knitr::opts_chunk$set(message=FALSE, warning=FALSE) # Introduction The `crisprViz` package enables the graphical interpretation of `GuideSet` -objects from the `crisprDesign` package by plotting guide RNA (gRNA) +objects from the [crisprDesign](https://github.com/crisprVerse/crisprDesign) package by plotting guide RNA (gRNA) cutting locations against their target gene or other genomic region. -These genomic plots are constructed using the `Gviz` package from Bioconductor. This vignette walks through several use cases that demonstrate the range of and how to use plotting functions in the `crisprViz` package. This vignette -also uses the `crisprDesign` package to manipulate `GuideSet` objects in -conjunction with plotting in the process of gRNA design. For more information -about the `crisprDesign` package see [vignettes]. +also uses our core gRNA design package [crisprDesign](https://github.com/crisprVerse/crisprDesign)to manipulate `GuideSet` objects in +conjunction with plotting in the process of gRNA design. + +Visit our [crisprVerse tutorial page](https://github.com/crisprVerse/Tutorials) to learn more about how to design gRNAs for different applications. + # Installation and getting started