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Updated vignette
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Jfortin1 committed Oct 17, 2022
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2 changes: 1 addition & 1 deletion DESCRIPTION
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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"))
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12 changes: 10 additions & 2 deletions README.Rmd
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Expand Up @@ -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

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56 changes: 30 additions & 26 deletions README.md
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Expand Up @@ -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

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## [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
Expand All @@ -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
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## [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
Expand All @@ -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
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11 changes: 6 additions & 5 deletions vignettes/intro.Rmd
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Expand Up @@ -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

Expand Down

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