Add eval = FALSE to code chunks not to be evaluated

README.Rmd

@@ -49,7 +49,7 @@ the JASPAR or the provided database.
 [`memes`](https://www.bioconductor.org/packages/release/bioc/html/memes.html)
 which relies on a local install of the
 [MEME suite](https://meme-suite.org/meme/), which can be installed as follows:
-```bash
+```{bash, eval = FALSE}
 MEME_VERSION=5.5.5  # or the latest version
 
 wget https://meme-suite.org/meme/meme-software/$MEME_VERSION/meme-$MEME_VERSION.tar.gz
@@ -69,18 +69,18 @@ source ~/.bashrc
 **NOTE:** It is important that Perl dependencies associated with MEME suite are
 also installed, particularly `XML::Parser`, which can be installed using the
 following command in the terminal:
-```bash
+```{bash, eval = FALSE}
 cpan install XML::Parser
 ```
 For more information, refer to the [Perl dependency section of the MEME suite](https://meme-suite.org/meme/doc/install.html#prereq_perl).
 
 Once the MEME suite and its associated Perl dependencies are installed, the
 development version of `MotifPeeker` can be installed using the following code:
-```R
+```{r, eval = FALSE}
 if(!require("remotes")) install.packages("remotes")
 
-remotes::install_github("`r paste(owner,repo,sep='/')`")
-library(`r pkg`)
+remotes::install_github("neurogenomics/MotifPeeker")
+library(MotifPeeker)
 ```
 
 Alternatively, you can use the [Docker/Singularity container](https://neurogenomics.github.io/MotifPeeker/articles/docker.html) to
@@ -97,7 +97,7 @@ run the package out-of-the-box.
 ## Usage
 
 Load the package and example datasets.  
-```R
+```{r, eval = FALSE}
 library(MotifPeeker)
 data("CTCF_ChIP_peaks", package = "MotifPeeker")
 data("CTCF_TIP_peaks", package = "MotifPeeker")
@@ -106,7 +106,7 @@ data("motif_MA1930.2", package = "MotifPeeker")
 ```
 
 Prepare input files.  
-```R
+```{r, eval = FALSE}
 peak_files <- list(CTCF_ChIP_peaks, CTCF_TIP_peaks)
 alignment_files <- list(
     system.file("extdata", "CTCF_ChIP_alignment.bam", package = "MotifPeeker"),
@@ -116,7 +116,7 @@ motif_files <- list(motif_MA1102.2, motif_MA1930.2)
 ```
 
 Run `MotifPeeker()`:  
-```R
+```{r, eval = FALSE}
 MotifPeeker(
     peak_files = peak_files,
     reference_index = 2,  # Set TIP-seq experiment as reference
@@ -142,8 +142,7 @@ MotifPeeker(
 
 These input parameters must be provided:  
 
-<details>
-<summary><strong>Details</strong></summary>
+<details><summary><strong>Details</strong></summary>
 
 - `peak_files`: A list of path to peak files or `GRanges` objects with the
   peaks to analyse. Currently, only peak files from `MACS2/3` (`.narrowPeak`)
@@ -165,8 +164,7 @@ These input parameters must be provided:
 These input parameters optional, but *recommended* to add more analyses, or
 enhance them:  
 
-<details>
-<summary><strong>Details</strong></summary>
+<details><summary><strong>Details</strong></summary>
 
 - `alignment_files`: A list of path to alignment files or `Rsamtools::BamFile`
   objects with the alignment sequences to analyse. Alignment files are used to
@@ -215,8 +213,7 @@ hours to complete.
 
 To make computation faster, we highly recommend tuning the following arguments:  
 
-<details>
-<summary><strong>Details</strong></summary>
+<details><summary><strong>Details</strong></summary>
 
 - `workers`: Running motif discovery in parallel can significantly reduce
   runtime, but it is very memory-intensive, consuming upwards of 10GB of RAM per
@@ -249,8 +246,7 @@ following files:
 
 `MotifPeeker` comes with several datasets bundled:  
 
-<details>
-<summary><strong>Details</strong></summary>
+<details><summary><strong>Details</strong></summary>
 
 - `CTCF_TIP_peaks`: Human CTCF peak file generated with TIP-seq using
   HCT116 cell-line. No control files were used to generate the peak file. The
@@ -281,6 +277,7 @@ to demonstrate the package and run tests to maintain the integrity of the
 package.
 
 ## Licensing Restrictions
+
 MotifPeeker incorporates the MEME Suite, which is available free of charge for
 educational, research, and non-profit purposes. Users intending to use
 MotifPeeker for commercial purposes are required to purchase a license for the

README.md

@@ -18,7 +18,7 @@ status](https://github.com/neurogenomics/MotifPeeker/workflows/rworkflows/badge.
 
 **Authors:** ***Hiranyamaya (Hiru) Dash, Thomas Roberts, Nathan
 Skene***  
-**Updated:** ***Jul-29-2024***
+**Updated:** ***Aug-05-2024***
 
 ## Introduction
 
@@ -374,18 +374,18 @@ utils::sessionInfo()
     ##  [1] gtable_0.3.5        jsonlite_1.8.8      renv_1.0.7         
     ##  [4] dplyr_1.1.4         compiler_4.4.1      BiocManager_1.30.23
     ##  [7] tidyselect_1.2.1    rvcheck_0.2.1       scales_1.3.0       
-    ## [10] yaml_2.3.9          fastmap_1.2.0       here_1.0.1         
+    ## [10] yaml_2.3.10         fastmap_1.2.0       here_1.0.1         
     ## [13] ggplot2_3.5.1       R6_2.5.1            generics_0.1.3     
     ## [16] knitr_1.48          yulab.utils_0.1.4   tibble_3.2.1       
     ## [19] desc_1.4.3          dlstats_0.1.7       rprojroot_2.0.4    
     ## [22] munsell_0.5.1       pillar_1.9.0        RColorBrewer_1.1-3 
     ## [25] rlang_1.1.4         utf8_1.2.4          cachem_1.1.0       
-    ## [28] badger_0.2.4        xfun_0.45           fs_1.6.4           
+    ## [28] badger_0.2.4        xfun_0.46           fs_1.6.4           
     ## [31] memoise_2.0.1       cli_3.6.3           magrittr_2.0.3     
     ## [34] rworkflows_1.0.1    digest_0.6.36       grid_4.4.1         
     ## [37] rstudioapi_0.16.0   lifecycle_1.0.4     vctrs_0.6.5        
     ## [40] data.table_1.15.4   evaluate_0.24.0     glue_1.7.0         
-    ## [43] fansi_1.0.6         colorspace_2.1-0    rmarkdown_2.27     
+    ## [43] fansi_1.0.6         colorspace_2.1-1    rmarkdown_2.27     
     ## [46] tools_4.4.1         pkgconfig_2.0.3     htmltools_0.5.8.1
 
 </details>

vignettes/MotifPeeker.Rmd

@@ -75,7 +75,7 @@ package.
 [`memes`](https://www.bioconductor.org/packages/release/bioc/html/memes.html)
 which relies on a local install of the
 [MEME suite](https://meme-suite.org/meme/), which can be installed as follows:
-```bash
+```{bash, eval = FALSE}
 MEME_VERSION=5.5.5  # or the latest version
 
 wget https://meme-suite.org/meme/meme-software/$MEME_VERSION/meme-$MEME_VERSION.tar.gz
@@ -95,15 +95,15 @@ source ~/.bashrc
 **NOTE:** It is important that Perl dependencies associated with MEME suite are
 also installed, particularly `XML::Parser`, which can be installed using the
 following command in the terminal:
-```bash
+```{bash, eval = FALSE}
 cpan install XML::Parser
 ```
 For more information, refer to the [Perl dependency section of the MEME suite](https://meme-suite.org/meme/doc/install.html#prereq_perl).
 
 Once the MEME suite and its associated Perl dependencies are installed, the
 latest development version of `MotifPeeker` can be installed using the following
 code:
-```R
+```{r, eval = FALSE}
 if(!require("remotes")) install.packages("remotes")
 
 remotes::install_github("neurogenomics/MotifPeeker")
@@ -142,7 +142,7 @@ data("motif_MA1930.2", package = "MotifPeeker")
 *MotifPeeker* accepts lists of both `GRanges` objects produced by
 `read_peak_file()`, or paths to the *MACS2/3* `.narrowPeak` files or *SEACR*
 `.bed` files, or ENCODE file IDs to automatically download the respective files.  
-```R
+```{r, eval = FALSE}
 ## MACS2/3 peak files
 peak_files <- list("/path/to/peak1.narrowPeak", "/path/to/peak2.narrowPeak")
 
@@ -173,7 +173,7 @@ alignment_files <- list(CTCF_ChIP_alignment, CTCF_TIP_alignment)
 ### Motif Files
 *MotifPeeker* accepts a list of either `universalmotif` objects, or paths to the
 `.jaspar` files.  
-```R
+```{r, eval = FALSE}
 ## JASPAR motif files
 motif_files <- list("/path/to/motif1.jaspar", "/path/to/motif2.jaspar")
 ```

vignettes/articles/docker.Rmd

@@ -19,7 +19,7 @@ vignette: |
 **Updated:** ***`r format(Sys.Date(), '%b-%d-%Y')`***  
 
 
-```{r setup, include=FALSE}
+```{r setup, include = FALSE}
 #### Package name ####
 PKG <- read.dcf("../../DESCRIPTION", fields = "Package")[1]
 library(PKG, character.only = TRUE)
@@ -39,9 +39,9 @@ docker_url <- if(grepl("ghcr.io",docker_registry)){
 
 # Installation 
 
-`r PKG` is now available via [`r docker_registry`](`r docker_url`) 
-as a containerised environment with Rstudio and 
-all necessary dependencies pre-installed.
+MotifPeeker is now available via
+[ghcr.io](https://ghcr.io/ghcr.io/neurogenomics/motifpeeker) as a containerised
+environment with Rstudio and  all necessary dependencies pre-installed.
 
 ## Method 1: via Docker
 
@@ -51,21 +51,21 @@ if you have not already.
 Create an image of the [Docker](https://www.docker.com/) container 
 in command line:  
 
-```bash
-docker pull `r cont`
+```{bash, eval = FALSE}
+docker pull ghcr.io/neurogenomics/motifpeeker
 ```
 
 Once the image has been created, you can launch it with:  
 
-```bash
+```{bash, eval = FALSE}
 docker run \
     -d \
     -e ROOT=true \
     -e PASSWORD="<your_password>" \
     -v ~/Desktop:/Desktop \
     -v /Volumes:/Volumes \
     -p 8900:8787 \
-    `r cont`
+    ghcr.io/neurogenomics/motifpeeker
 ```  
 
 ### NOTES
@@ -86,8 +86,8 @@ If you are using a system that does not allow Docker
 (as is the case for many institutional computing clusters), 
 you can instead [install Docker images via Singularity](https://docs.sylabs.io/guides/2.6/user-guide/singularity_and_docker.html).  
 
-```bash
-singularity pull docker://`r cont`
+```{bash, eval = FALSE}
+singularity pull docker://ghcr.io/neurogenomics/motifpeeker
 ```
 
 For troubleshooting, see the [Singularity documentation](https://docs.sylabs.io/guides/latest/user-guide/singularity_and_docker.html#github-container-registry).

vignettes/articles/examples.Rmd

@@ -39,7 +39,7 @@ HCT116 cells. Details of the datasets used are as follows:
 
 Peak calling was performed using
 [`MACS3`](https://github.com/macs3-project/MACS) using the following commands:
-```R
+```{r, eval = FALSE}
 ## For ChIP-Seq datasets
 MACSr::callpeak(
         tfile = ...,