Updated vignette

crisprVerse · Oct 17, 2022 · 4f355a4 · 4f355a4
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: crisprBowtie
-Version: 1.1.1
-Date: 2022-03-08
+Version: 1.1.2
+Date: 2022-10-17
 Title: Bowtie-based alignment of CRISPR gRNA spacer sequences
 Authors@R: c(
     person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre")))

diff --git a/README.Rmd b/README.Rmd
@@ -18,18 +18,21 @@ Date: July 13, 2022
 `crisprBowtie` provides two main functions to align short DNA sequences to
 a reference genome using the short read aligner bowtie [@langmead2009bowtie]
 and return the alignments as R objects: `runBowtie` and `runCrisprBowtie`.
-It utilizes the Bioconductor package `Rbowtie` to access the bowtie program
+It utilizes the Bioconductor package `Rbowtie` to access the Bowtie program
 in a platform-independent manner. This means that users do not need to install
-bowtie prior to using `crisprBowtie`. 
+Bowtie prior to using `crisprBowtie`. 
 
 
 The latter function (`runCrisprBowtie`) is specifically designed
 to map and annotate CRISPR guide RNA (gRNA) spacer sequences using
 CRISPR nuclease objects and CRISPR genomic arithmetics defined in
-the Bioconductor `crisprBase` package. This enables a fast and accurate
-on-target and off-target search of gRNA spacer sequences for virtually any
-type of CRISPR nucleases. 
-
+the Bioconductor package
+[crisprBase](https://github.com/crisprVerse/crisprBase).
+This enables a fast and accurate on-target and off-target search of 
+gRNA spacer sequences for virtually any type of CRISPR nucleases. 
+It also provides an off-target search engine for our main gRNA design package [crisprDesign](https://github.com/crisprVerse/crisprDesign) of the 
+[crisprVerse](https://github.com/crisprVerse) ecosystem. See the 
+`addSpacerAlignments` function in `crisprDesign` for more details. 
 
 
 # Installation and getting started
@@ -41,11 +44,6 @@ type of CRISPR nucleases.
 This package is supported for macOS, Linux and Windows machines.
 Package was developed and tested on R version 4.2.1.
 
-### R Dependencies 
-
-- crisprBase: https://github.com/Jfortin1/crisprBase
-- RBowtie: https://bioconductor.org/packages/release/bioc/html/Rbowtie.html
-
 
 ## Installation from Bioconductor
 
@@ -64,33 +62,14 @@ The complete documentation for the package can be found [here](https://bioconduc
 
 
 
-## Installation from GitHub
-
-Alternatively, `crisprBowtie` and its dependencies can be installed by typing the
-following commands inside of an R session:
-
-
-```r
-install.packages("BiocManager")
-install.packages("devtools")
-BiocManager::install("Rbowtie")
-devtools::install_github("crisprVerse/crisprBase")
-devtools::install_github("crisprVerse/crisprBowtie")
-```
-
-
-
-
-
-
 # Building a bowtie index
 
-To use `runBowtie` or `runCrisprBowtie`, users need to first build a bowtie
+To use `runBowtie` or `runCrisprBowtie`, users need to first build a Bowtie
 genome index. For a given genome, this step has to be done only once. 
-The `Rbowtie` package convenitenly provides the function `bowtie_build`
-to build a bowtie index from any custom genome from a FASTA file.
+The `Rbowtie` package conveniently provides the function `bowtie_build`
+to build a Bowtie index from any custom genome from a FASTA file.
 
-As an example, we build a bowtie index for a small portion of the human
+As an example, we build a Bowtie index for a small portion of the human
 chromosome 1 (`chr1.fa` file provided in the `crisprBowtie` package) and
 save the index file as `myIndex` to a temporary directory:
 
@@ -104,6 +83,11 @@ Rbowtie::bowtie_build(fasta,
                       prefix="myIndex")
 ```
 
+To learn how to create a Bowtie index for a complete genome or transcriptome,
+please visit our [tutorial page](https://github.com/crisprVerse/Tutorials/tree/master/Building_Genome_Indices).
+
+
+
 # Alignment using `runCrisprBowtie`
 
 As an example, we align 6 spacer sequences (of length 20bp) to the
@@ -117,7 +101,7 @@ non-canonical PAM sequences are also considered (NAG and NGA for SpCas9).
 The function `getAvailableCrisprNucleases` in `crisprBase` returns a character
 vector of available `crisprNuclease` objects found in `crisprBase`. 
 
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(crisprBowtie)
 data(SpCas9, package="crisprBase")
 crisprNuclease <- SpCas9

diff --git a/README.md b/README.md
@@ -9,12 +9,9 @@ crisprBowtie: alignment of gRNA spacer sequences using bowtie
     -   <a href="#software-requirements" id="toc-software-requirements">Software
         requirements</a>
         -   <a href="#os-requirements" id="toc-os-requirements">OS Requirements</a>
-        -   <a href="#r-dependencies" id="toc-r-dependencies">R Dependencies</a>
     -   <a href="#installation-from-bioconductor"
         id="toc-installation-from-bioconductor">Installation from
         Bioconductor</a>
-    -   <a href="#installation-from-github"
-        id="toc-installation-from-github">Installation from GitHub</a>
 -   <a href="#building-a-bowtie-index"
     id="toc-building-a-bowtie-index">Building a bowtie index</a>
 -   <a href="#alignment-using-runcrisprbowtie"
@@ -38,15 +35,20 @@ Date: July 13, 2022
 to a reference genome using the short read aligner bowtie (Langmead et
 al. 2009) and return the alignments as R objects: `runBowtie` and
 `runCrisprBowtie`. It utilizes the Bioconductor package `Rbowtie` to
-access the bowtie program in a platform-independent manner. This means
-that users do not need to install bowtie prior to using `crisprBowtie`.
+access the Bowtie program in a platform-independent manner. This means
+that users do not need to install Bowtie prior to using `crisprBowtie`.
 
 The latter function (`runCrisprBowtie`) is specifically designed to map
 and annotate CRISPR guide RNA (gRNA) spacer sequences using CRISPR
 nuclease objects and CRISPR genomic arithmetics defined in the
-Bioconductor `crisprBase` package. This enables a fast and accurate
-on-target and off-target search of gRNA spacer sequences for virtually
-any type of CRISPR nucleases.
+Bioconductor package
+[crisprBase](https://github.com/crisprVerse/crisprBase). This enables a
+fast and accurate on-target and off-target search of gRNA spacer
+sequences for virtually any type of CRISPR nucleases. It also provides
+an off-target search engine for our main gRNA design package
+[crisprDesign](https://github.com/crisprVerse/crisprDesign) of the
+[crisprVerse](https://github.com/crisprVerse) ecosystem. See the
+`addSpacerAlignments` function in `crisprDesign` for more details.
 
 # Installation and getting started
 
@@ -57,12 +59,6 @@ any type of CRISPR nucleases.
 This package is supported for macOS, Linux and Windows machines. Package
 was developed and tested on R version 4.2.1.
 
-### R Dependencies
-
--   crisprBase: <https://github.com/Jfortin1/crisprBase>
--   RBowtie:
-    <https://bioconductor.org/packages/release/bioc/html/Rbowtie.html>
-
 ## Installation from Bioconductor
 
 `crisprBowtie` can be installed from from the Bioconductor devel branch
@@ -79,28 +75,15 @@ BiocManager::install("crisprBowtie")
 The complete documentation for the package can be found
 [here](https://bioconductor.org/packages/devel/bioc/manuals/crisprBowtie/man/crisprBowtie.pdf).
 
-## Installation from GitHub
-
-Alternatively, `crisprBowtie` and its dependencies can be installed by
-typing the following commands inside of an R session:
-
-``` r
-install.packages("BiocManager")
-install.packages("devtools")
-BiocManager::install("Rbowtie")
-devtools::install_github("crisprVerse/crisprBase")
-devtools::install_github("crisprVerse/crisprBowtie")
-```
-
 # Building a bowtie index
 
 To use `runBowtie` or `runCrisprBowtie`, users need to first build a
-bowtie genome index. For a given genome, this step has to be done only
-once. The `Rbowtie` package convenitenly provides the function
-`bowtie_build` to build a bowtie index from any custom genome from a
+Bowtie genome index. For a given genome, this step has to be done only
+once. The `Rbowtie` package conveniently provides the function
+`bowtie_build` to build a Bowtie index from any custom genome from a
 FASTA file.
 
-As an example, we build a bowtie index for a small portion of the human
+As an example, we build a Bowtie index for a small portion of the human
 chromosome 1 (`chr1.fa` file provided in the `crisprBowtie` package) and
 save the index file as `myIndex` to a temporary directory:
 
@@ -114,6 +97,10 @@ Rbowtie::bowtie_build(fasta,
                       prefix="myIndex")
 ```
 
+To learn how to create a Bowtie index for a complete genome or
+transcriptome, please visit our [tutorial
+page](https://github.com/crisprVerse/Tutorials/tree/master/Building_Genome_Indices).
+
 # Alignment using `runCrisprBowtie`
 
 As an example, we align 6 spacer sequences (of length 20bp) to the
@@ -212,38 +199,38 @@ sessionInfo()
     ## [1] crisprBowtie_1.1.1 Rbowtie_1.37.0    
     ## 
     ## loaded via a namespace (and not attached):
-    ##  [1] SummarizedExperiment_1.27.1 tidyselect_1.1.2           
+    ##  [1] SummarizedExperiment_1.27.2 tidyselect_1.1.2           
     ##  [3] xfun_0.32                   purrr_0.3.4                
     ##  [5] lattice_0.20-45             vctrs_0.4.1                
     ##  [7] htmltools_0.5.3             stats4_4.2.1               
     ##  [9] rtracklayer_1.57.0          yaml_2.3.5                 
     ## [11] utf8_1.2.2                  XML_3.99-0.10              
-    ## [13] rlang_1.0.4                 pillar_1.8.1               
+    ## [13] rlang_1.0.5                 pillar_1.8.1               
     ## [15] glue_1.6.2                  BiocParallel_1.31.12       
-    ## [17] bit64_4.0.5                 BiocGenerics_0.43.1        
+    ## [17] bit64_4.0.5                 BiocGenerics_0.43.4        
     ## [19] matrixStats_0.62.0          GenomeInfoDbData_1.2.8     
     ## [21] lifecycle_1.0.1             stringr_1.4.1              
     ## [23] zlibbioc_1.43.0             MatrixGenerics_1.9.1       
-    ## [25] Biostrings_2.65.2           codetools_0.2-18           
+    ## [25] Biostrings_2.65.3           codetools_0.2-18           
     ## [27] evaluate_0.16               restfulr_0.0.15            
     ## [29] Biobase_2.57.1              knitr_1.40                 
     ## [31] tzdb_0.3.0                  IRanges_2.31.2             
-    ## [33] fastmap_1.1.0               GenomeInfoDb_1.33.5        
+    ## [33] fastmap_1.1.0               GenomeInfoDb_1.33.7        
     ## [35] parallel_4.2.1              fansi_1.0.3                
-    ## [37] crisprBase_1.1.5            readr_2.1.2                
+    ## [37] crisprBase_1.1.8            readr_2.1.2                
     ## [39] BSgenome_1.65.2             DelayedArray_0.23.1        
-    ## [41] S4Vectors_0.35.1            vroom_1.5.7                
-    ## [43] XVector_0.37.0              bit_4.0.4                  
+    ## [41] S4Vectors_0.35.3            vroom_1.5.7                
+    ## [43] XVector_0.37.1              bit_4.0.4                  
     ## [45] Rsamtools_2.13.4            rjson_0.2.21               
     ## [47] hms_1.1.2                   digest_0.6.29              
     ## [49] stringi_1.7.8               BiocIO_1.7.1               
     ## [51] GenomicRanges_1.49.1        grid_4.2.1                 
-    ## [53] cli_3.3.0                   tools_4.2.1                
+    ## [53] cli_3.4.0                   tools_4.2.1                
     ## [55] bitops_1.0-7                magrittr_2.0.3             
     ## [57] RCurl_1.98-1.8              tibble_3.1.8               
     ## [59] crayon_1.5.1                pkgconfig_2.0.3            
     ## [61] ellipsis_0.3.2              Matrix_1.4-1               
-    ## [63] rmarkdown_2.15.2            rstudioapi_0.14            
+    ## [63] rmarkdown_2.16              rstudioapi_0.14            
     ## [65] R6_2.5.1                    GenomicAlignments_1.33.1   
     ## [67] compiler_4.2.1
 

diff --git a/vignettes/crisprBowtie.Rmd b/vignettes/crisprBowtie.Rmd
@@ -25,18 +25,21 @@ bibliography: references.bib
 `crisprBowtie` provides two main functions to align short DNA sequences to
 a reference genome using the short read aligner bowtie [@langmead2009bowtie]
 and return the alignments as R objects: `runBowtie` and `runCrisprBowtie`.
-It utilizes the Bioconductor package `Rbowtie` to access the bowtie program
+It utilizes the Bioconductor package `Rbowtie` to access the Bowtie program
 in a platform-independent manner. This means that users do not need to install
-bowtie prior to using `crisprBowtie`. 
+Bowtie prior to using `crisprBowtie`. 
 
 
 The latter function (`runCrisprBowtie`) is specifically designed
 to map and annotate CRISPR guide RNA (gRNA) spacer sequences using
 CRISPR nuclease objects and CRISPR genomic arithmetics defined in
-the Bioconductor `crisprBase` package. This enables a fast and accurate
-on-target and off-target search of gRNA spacer sequences for virtually any
-type of CRISPR nucleases. 
-
+the Bioconductor package
+[crisprBase](https://github.com/crisprVerse/crisprBase).
+This enables a fast and accurate on-target and off-target search of 
+gRNA spacer sequences for virtually any type of CRISPR nucleases. 
+It also provides an off-target search engine for our main gRNA design package [crisprDesign](https://github.com/crisprVerse/crisprDesign) of the 
+[crisprVerse](https://github.com/crisprVerse) ecosystem. See the 
+`addSpacerAlignments` function in `crisprDesign` for more details. 
 
 
 # Installation and getting started
@@ -48,13 +51,6 @@ type of CRISPR nucleases.
 This package is supported for macOS, Linux and Windows machines.
 Package was developed and tested on R version 4.2.
 
-### R Dependencies 
-
-- crisprBase: https://github.com/Jfortin1/crisprBase
-- RBowtie: https://bioconductor.org/packages/release/bioc/html/Rbowtie.html
-
-
-
 
 ## Installation from Bioconductor
 
@@ -74,12 +70,12 @@ BiocManager::install("crisprBowtie")
 
 # Building a bowtie index
 
-To use `runBowtie` or `runCrisprBowtie`, users need to first build a bowtie
+To use `runBowtie` or `runCrisprBowtie`, users need to first build a Bowtie
 genome index. For a given genome, this step has to be done only once. 
-The `Rbowtie` package convenitenly provides the function `bowtie_build`
-to build a bowtie index from any custom genome from a FASTA file.
+The `Rbowtie` package conveniently provides the function `bowtie_build`
+to build a Bowtie index from any custom genome from a FASTA file.
 
-As an example, we build a bowtie index for a small portion of the human
+As an example, we build a Bowtie index for a small portion of the human
 chromosome 1 (`chr1.fa` file provided in the `crisprBowtie` package) and
 save the index file as `myIndex` to a temporary directory:
 
@@ -93,6 +89,11 @@ Rbowtie::bowtie_build(fasta,
                       prefix="myIndex")
 ```
 
+To learn how to create a Bowtie index for a complete genome or transcriptome,
+please visit our [tutorial page](https://github.com/crisprVerse/Tutorials/tree/master/Building_Genome_Indices).
+
+
+
 # Alignment using `runCrisprBowtie`
 
 As an example, we align 6 spacer sequences (of length 20bp) to the
@@ -106,7 +107,7 @@ non-canonical PAM sequences are also considered (NAG and NGA for SpCas9).
 The function `getAvailableCrisprNucleases` in `crisprBase` returns a character
 vector of available `crisprNuclease` objects found in `crisprBase`. 
 
-```{r}
+```{r, warning=FALSE, message=FALSE}
 library(crisprBowtie)
 data(SpCas9, package="crisprBase")
 crisprNuclease <- SpCas9