### Install methylclock Package

Source: https://github.com/isglobal-brge/methylclock/blob/main/vignettes/methylclock.html

Installs the methylclock package from GitHub. Ensure devtools is installed first.

```R
library(devtools)
install_github("isglobal-brge/methylclock")
```

--------------------------------

### Install MethylClock Package

Source: https://github.com/isglobal-brge/methylclock/blob/main/vignettes/methylclock_old_Bioinf.html

Installs the methylclock package from GitHub using devtools. This should be run after installing dependencies.

```R
install_github("isglobal-brge/methylclock")
```

--------------------------------

### Install MethylClock Dependencies

Source: https://github.com/isglobal-brge/methylclock/blob/main/vignettes/methylclock_old_Bioinf.html

Installs necessary R packages from BiocManager and GitHub. Ensure BiocManager is installed before running.

```R
library(BiocManager)
install(c("tidyverse", "impute", "Rcpp", "GAprediction"))
```

```R
library(devtools)
install_github("perishky/meffil")
```

--------------------------------

### Install methylclock for R >= 4.1 (Bioconductor)

Source: https://github.com/isglobal-brge/methylclock/blob/main/README.md

Install the Bioconductor version of methylclock for R version 4.1 and above. Ensure BiocManager is installed first.

```r
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("methylclock")

```

--------------------------------

### JSONP Request Setup

Source: https://github.com/isglobal-brge/methylclock/blob/main/vignettes/methylclock_old_Bioinf.html

Configures jQuery to handle JSONP requests. It dynamically creates a callback function and manages the script loading.

```javascript
var _b=[],ac=/(=)\?(?=&|$)|\?\?/;m.ajaxSetup({jsonp:"callback",jsonpCallback:function(){var a=_b.pop()||m.expando+"_"+vb++;return this[a]=!0,a}}),m.ajaxPrefilter("json jsonp",function(b,c,d){var e,f,g,h=b.jsonp!==!1&&(ac.test(b.url)?"url":"string"==typeof b.data&&!(b.contentType||"").indexOf("application/x-www-form-urlencoded")&&ac.test(b.data)&&"data");return h||"jsonp"===b.dataTypes[0]?(e=b.jsonpCallback=m.isFunction(b.jsonpCallback)?b.jsonpCallback():b.jsonpCallback,h?b[h]=b[h].replace(ac,"$1"+e):b.jsonp!==!1&&(b.url+=(wb.test(b.url)?"&":"?")+b.jsonp+"="+e),b.converters["script json"]=function(){return g||m.error(e+" was not called"),g[0]},b.dataTypes[0]="json",f=a[e],a[e]=function(){g=arguments},d.always(function(){a[e]=
```

--------------------------------

### Install methylclock for R < 4.1

Source: https://github.com/isglobal-brge/methylclock/blob/main/README.md

Use this command to install the methylclock package from the main branch for R versions prior to 4.1.

```r
library(devtools)

install_github("isglobal-brge/methylclock@main")

```

--------------------------------

### Install Required R Packages

Source: https://github.com/isglobal-brge/methylclock/blob/main/vignettes/methylclock.html

Installs essential R packages for the methylclock package, including tidyverse, impute, and Rcpp.

```R
library(BiocManager)
install(c("tidyverse", "impute", "Rcpp"))
```

--------------------------------

### Load Document Reproduction Libraries

Source: https://github.com/isglobal-brge/methylclock/blob/main/vignettes/methylclock_old_Bioinf.html

Loads R libraries required for reproducing the documentation examples. Includes packages for data manipulation, plotting, and bioinformatics.

```R
library(Biobase)
library(tibble)
library(ggplot2)
library(ggpmisc)
library(GEOquery)
```

--------------------------------

### Initialize Syntax Highlighting

Source: https://github.com/isglobal-brge/methylclock/blob/main/vignettes/methylclock.html

Configures and initializes Highlight.js for code block rendering.

```javascript
if (window.hljs) { hljs.configure({languages: []}); hljs.initHighlightingOnLoad(); if (document.readyState && document.readyState === "complete") { window.setTimeout(function() { hljs.initHighlighting(); }, 0); } }
```

--------------------------------

### Initialize Respond.js Polyfill

Source: https://github.com/isglobal-brge/methylclock/blob/main/vignettes/methylclock_old_Bioinf.html

This script provides media query support for IE8 and below by polyfilling matchMedia and parsing CSS media queries.

```javascript
if (!!window.navigator.userAgent.match("MSIE 8")) { !function(a){"use strict";a.matchMedia=a.matchMedia||function(a){var b,c=a.documentElement,d=c.firstElementChild||c.firstChild,e=a.createElement("body"),f=a.createElement("div");return f.id="mq-test-1",f.style.cssText="position:absolute;top:-100em",e.style.background="none",e.appendChild(f),function(a){return f.innerHTML='&shy;<style media="'+a+'"> #mq-test-1 { width: 42px; }</style>',c.insertBefore(e,d),b=42===f.offsetWidth,c.removeChild(e),{matches:b,media:a}}}(a.document)}(this),function(a){"use strict";function b(){u(!0)}var c={};a.respond=c,c.update=function(){};var d=[],e=function(){var b=!1;try{b=new a.XMLHttpRequest}catch(c){b=new a.ActiveXObject("Microsoft.XMLHTTP")}return function(){return b}}(),f=function(a,b){var c=e();c&&(c.open("GET",a,!0),c.onreadystatechange=function(){4!==c.readyState||200!==c.status&&304!==c.status||b(c.responseText)},4!==c.readyState&&c.send(null))};if(c.ajax=f,c.queue=d,c.regex={media:/@media[^\{]+\{([^\{\}]*\{[^\}\{]*\})+/gi,keyframes:/@(?:\-(?:o|moz|webkit)\-)?keyframes[^\{]+\{(?:[^\{\}]*\{[^\}\{]*\})+[^\}]*\}/gi,urls:/(url\()['"]?([^/\)'"]+[^:\)'"]+)['"]?(\))/g,findStyles:/@media *([^\{]+)\{([\S\s]+?)$/,only:/(only\s+)?([a-zA-Z]+)\s?/,minw:/\(\s*min\-width\s*:\s*(\s*[0-9\.]+)(px|em)\s*\)/,maxw:/\(\s*max\-width\s*:\s*(\s*[0-9\.]+)(px|em)\s*\)/},c.mediaQueriesSupported=a.matchMedia&&null!==a.matchMedia("only all")&&a.matchMedia("only all").matches,!c.mediaQueriesSupported){var g,h,i,j=a.document,k=j.documentElement,l=[],m=[],n=[],o={},p=30,q=j.getElementsByTagName("head")[0]||k,r=j.getElementsByTagName("base")[0],s=q.getElementsByTagName("link"),t=function(){var a,b=j.createElement("div"),c=j.body,d=k.style.fontSize,e=c&&c.style.fontSize,f=!1;return b.style.cssText="position:absolute;font-size:1em;width:1em",c||(c=f=j.createElement("body"),c.style.background="none"),k.style.fontSize="100%",c.style.fontSize="100%",c.appendChild(b),f&&k.insertBefore(c,k.firstChild),a=b.offsetWidth,f?k.removeChild(c):c.removeChild(b),k.style.fontSize=d,e&&(c.style.fontSize=e),a=i=parseFloat(a)},u=function(b){var c="clientWidth",d=k[c],e="CSS1Compat"===j.compatMode&&d||j.body[c]||d,f={},o=s[s.length-1],r=(new Date).getTime();if(b&&g&&p>r-g)return a.clearTimeout(h),h=a.setTimeout(u,p),void 0;g=r;for(var v in l)if(l.hasOwnProperty(v)){var w=l[v],x=w.minw,y=w.maxw,z=null===x,A=null===y,B="em";x&&(x=parseFloat(x)*(x.indexOf(B)>-1?i||t():1)),y&&(y=parseFloat(y)*(y.indexOf(B)>-1?i||t():1)),w.hasquery&&(z&&A||!(z||e>=x)||!(A||y>=e))||(f[w.media]||(f[w.media]=[]),f[w.media].push(m[w.rules
```