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d,h as v,m as g,d as m,c as S,i as _,x,n as E,y as $,z as q}from"../chunks/scheduler.a30ae394.js";import{S as z,i as C}from"../chunks/index.49b3fccf.js";import{p as H}from"../chunks/stores.f695ab5d.js";function P(i){var f;let a,s=i[0].status+"",r,o,n,p=((f=i[0].error)==null?void 0:f.message)+"",c;return{c(){a=u("h1"),r=h(s),o=y(),n=u("p"),c=h(p)},l(e){a=d(e,"H1",{});var t=v(a);r=g(t,s),t.forEach(m),o=S(e),n=d(e,"P",{});var l=v(n);c=g(l,p),l.forEach(m)},m(e,t){_(e,a,t),x(a,r),_(e,o,t),_(e,n,t),x(n,c)},p(e,[t]){var l;t&1&&s!==(s=e[0].status+"")&&E(r,s),t&1&&p!==(p=((l=e[0].error)==null?void 0:l.message)+"")&&E(c,p)},i:$,o:$,d(e){e&&(m(a),m(o),m(n))}}}function j(i,a,s){let r;return q(i,H,o=>s(0,r=o)),[r]}class B extends z{constructor(a){super(),C(this,a,j,P,b,{})}}export{B as component}; +import{s as b,f as u,l as h,a as y,g as d,h as v,m as g,d as m,c as S,i as _,x,n as E,y as $,z as q}from"../chunks/scheduler.a30ae394.js";import{S as z,i as C}from"../chunks/index.49b3fccf.js";import{p 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GOAT online geneset enrichment analysis

Identify enriched genesets in a preranked genelist generated by e.g. proteomics or gene +import{s as Xe,f as t,a as r,l as ee,A as Je,g as s,d as n,c as l,h,m as te,B as x,j as a,C as se,D as Q,k as d,x as e,i as X,y as Ae,z as Qe}from"../chunks/scheduler.a30ae394.js";import{S as We,i as Ye}from"../chunks/index.49b3fccf.js";/* empty css */import{p as Ze}from"../chunks/stores.b6b25a96.js";import{e as Ue}from"../chunks/singletons.3d14f100.js";function et(o){let b,B,i,p,f,y,W,ae,A,ne,ie,O,re,le,T,oe,de,C,ce,Y,q,Oe=`

GOAT online geneset enrichment analysis

Identify enriched genesets in a preranked genelist generated by e.g. proteomics or gene expression studies using the GOAT algorithm.

`,Z,g,M,Te=`

The GOAT algorithm for geneset enrichment analysis

The GOAT algorithm has not been published yet but a preprint is available, please cite it when using the early-access version of GOAT;
Koopmans, F. (2023). GOAT: efficient and robust identification of geneset enrichment.
https://doi.org/10.1101/2023.12.10.570979

GOAT features: @@ -23,4 +23,4 @@ import{s as Xe,f as t,a as r,l as ee,A as Je,g as s,d as n,c as l,h,m as te,B as scores. The result is a skewed gene score distribution.
  • For each geneset size N (number of genes), bootstrapping procedures generate a null distribution of geneset scores. This yields a skewed-normal distribution for small genesets and converges to a normal distribution for large genesets.
  • Geneset significance is determined for each geneset by comparing its score (mean of - respective gene scores) against a null distribution of the same size (N).
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    Citation

    The GOAT algorithm has not been published yet but a preprint is available, please cite it when +import{s as le,f as o,a as l,A as re,g as n,d as t,c as r,h as ne,B as u,j as k,D as O,k as p,x as d,i as s,y as S,z as ue}from"../chunks/scheduler.a30ae394.js";import{S as pe,i as he}from"../chunks/index.49b3fccf.js";/* empty css */import{p as de}from"../chunks/stores.b6b25a96.js";import{e as w}from"../chunks/singletons.3d14f100.js";function ce(x){let m,I,a,h,g,D=`GOAT`,K,v,$="Home",R,f,Y="GOAT online",W,y,J="gene ID mapping",B,b,Q="Documentation",E,M,U="Documentation",L,H,Z=`

    Citation

    The GOAT algorithm has not been published yet but a preprint is available, please cite it when using the early-access version of GOAT;
    Koopmans, F. (2023). GOAT: efficient and robust identification of geneset enrichment.
    https://doi.org/10.1101/2023.12.10.570979

    A ready-made M&M text describing your GOAT analysis is included with this tool's results (c.f. the log file contained in the output ZIP-file).

    `,P,T,X='

    How do I use this tool?

    brief overview of workflow
    1. input data: genelist
    2. input data: genesets
    3. settings
    4. start
    5. view summary table + download link (contains Excel table and M&M for your paper)
    6. use interactive data analysis tools to inspect results

    Can I use the GOAT algorithm programmatically?
    Yes! We also provide a R package; via this link
    ',z,_,ee=`

    Expected file format for the input genelist:

    • File format: either CSV, TSV or Excel (.xlsx file, data on the first sheet). Note that for diff --git a/_app/immutable/nodes/3.7da57ec3.js.br b/_app/immutable/nodes/3.7da57ec3.js.br new file mode 100644 index 0000000..cc06330 Binary files /dev/null and b/_app/immutable/nodes/3.7da57ec3.js.br differ diff --git a/_app/immutable/nodes/3.7da57ec3.js.gz b/_app/immutable/nodes/3.7da57ec3.js.gz new file mode 100644 index 0000000..bae90c4 Binary files /dev/null and b/_app/immutable/nodes/3.7da57ec3.js.gz differ diff --git a/_app/immutable/nodes/4.63d47e78.js.br b/_app/immutable/nodes/4.63d47e78.js.br deleted file mode 100644 index 6b4e142..0000000 Binary files a/_app/immutable/nodes/4.63d47e78.js.br and /dev/null differ diff --git a/_app/immutable/nodes/4.63d47e78.js.gz b/_app/immutable/nodes/4.63d47e78.js.gz deleted file mode 100644 index b1d2327..0000000 Binary files a/_app/immutable/nodes/4.63d47e78.js.gz and /dev/null differ diff --git a/_app/immutable/nodes/4.63d47e78.js b/_app/immutable/nodes/4.ed4fb29d.js similarity index 99% rename from _app/immutable/nodes/4.63d47e78.js rename to _app/immutable/nodes/4.ed4fb29d.js index 8f972e8..878e158 100644 --- a/_app/immutable/nodes/4.63d47e78.js +++ b/_app/immutable/nodes/4.ed4fb29d.js @@ -1,4 +1,4 @@ -import{s as mn,p as Jt,E as bn,f as d,a as y,l as P,A as vn,g as c,d as n,c as w,h as A,B as V,m as W,j as _,D as Ie,k as B,F as Xe,x as s,i as b,G,H as Qt,I as gn,z as $e,n as Ce,y as fn,e as Xt}from"../chunks/scheduler.a30ae394.js";import{S as _n,i as yn,f as $t,b as en,d as tn,m as nn,a as ln,t as sn,e as an}from"../chunks/index.49b3fccf.js";import{p as wn,S as on,g as In,f as Cn,a as kn,d as Tn,c as xn,F as An,l as En}from"../chunks/stores.4b0fba64.js";/* empty css */import{p as Rn}from"../chunks/stores.f695ab5d.js";import{e as ce,w as rn}from"../chunks/singletons.78e1560b.js";function Gn(e){const t=e.length,r=e[0].map(a=>a.toLowerCase()),f=r.indexOf("symbol");let l;const p=f+1,i=[];if(f===-1)throw new Error("input genelist table must contain headers on the first line. Cannot find required header for column; 'symbol' (should contain character/string values)");if(r.filter(a=>a==="symbol").length>1)throw new Error("input genelist table is invalid because it contains multiple columns with the name 'symbol' (remove redundant columns)");for(let a=1;aa.length>=2&&f.test(a)===!1))],p=[],i=e.length;for(let a=0;am.length>=2),T=h.length;let I;if(T===1)I=t[h[0]];else if(T>1&&r!=="skipAmbiguous")if(r==="retainFirstSucces")for(let m=0;m0){a=a.reverse();for(let u=0;ua.toLowerCase()),f=r.indexOf("symbol");let l;const p=f+1,i=[];if(f===-1)throw new Error("input genelist table must contain headers on the first line. Cannot find required header for column; 'symbol' (should contain character/string values)");if(r.filter(a=>a==="symbol").length>1)throw new Error("input genelist table is invalid because it contains multiple columns with the name 'symbol' (remove redundant columns)");for(let a=1;aa.length>=2&&f.test(a)===!1))],p=[],i=e.length;for(let a=0;am.length>=2),T=h.length;let I;if(T===1)I=t[h[0]];else if(T>1&&r!=="skipAmbiguous")if(r==="retainFirstSucces")for(let m=0;m0){a=a.reverse();for(let u=0;u`,a,h,T="Home",I,m,u="GOAT online",R,v,E="gene ID mapping",ee,j,S="Documentation",C,x,he=`

      Gene ID mapping

      With this tool you can map gene symbols in an Excel/CSV/TSV table to Human gene identifiers.
      diff --git a/_app/immutable/nodes/4.ed4fb29d.js.br b/_app/immutable/nodes/4.ed4fb29d.js.br new file mode 100644 index 0000000..7c67bb3 Binary files /dev/null and b/_app/immutable/nodes/4.ed4fb29d.js.br differ diff --git a/_app/immutable/nodes/4.ed4fb29d.js.gz b/_app/immutable/nodes/4.ed4fb29d.js.gz new file mode 100644 index 0000000..2fe18f0 Binary files /dev/null and b/_app/immutable/nodes/4.ed4fb29d.js.gz differ diff --git a/_app/immutable/nodes/5.57e59d04.js b/_app/immutable/nodes/5.4e61c7dc.js similarity index 99% rename from _app/immutable/nodes/5.57e59d04.js rename to _app/immutable/nodes/5.4e61c7dc.js index 3666778..490c537 100644 --- a/_app/immutable/nodes/5.57e59d04.js +++ b/_app/immutable/nodes/5.4e61c7dc.js @@ -1,4 +1,4 @@ -import{y as it,I as bt,J as gu,K as jo,L as pu,M as Ma,s as Xt,l as Se,m as ke,i as le,n as Ge,d as A,e as Ft,z as gt,f as T,g as x,B as be,a as K,h as q,c as J,j as D,k as Ce,D as de,x as w,N as ui,G as _e,O as lt,F as Nt,q as fi,P as mu,Q as Uo,R as _u,S as vu,p as _t,T as ft,U as dt,V as di,W as Pa,X as bu,t as wu,H as It,A as yu,Y as Su}from"../chunks/scheduler.a30ae394.js";import{S as Ut,i as Yt,b as Ye,d as tt,m as Ke,a as xe,t as Ne,e as Je,g as Gt,c as jt,f as zt}from"../chunks/index.49b3fccf.js";import{c as ku,b as wi,e as $r,h as ei,i as Cu,j as We,n as qo,k as Ru,d as Oa,F as Ba,S as pr,g as Eu,m as Wo,o as Au,u as Iu,q as zu,r as vs,s as Fu,t as Du,v as Tu,w as xu,x as Mu,y as Pu,z as Ou,A as Bu,B as Vu,C as Nu,D as Hu,E as Lu,a as Gu,G as ju,H as Uu,I as qu,J as Wu}from"../chunks/stores.4b0fba64.js";/* empty css */import{p as Zu}from"../chunks/stores.f695ab5d.js";import{r as Zo,w as mn,j as Xu,e as _n}from"../chunks/singletons.78e1560b.js";const Va=typeof window<"u";let Xo=Va?()=>window.performance.now():()=>Date.now(),Na=Va?e=>requestAnimationFrame(e):it;const _r=new Set;function Ha(e){_r.forEach(t=>{t.c(e)||(_r.delete(t),t.f())}),_r.size!==0&&Na(Ha)}function Yu(e){let t;return _r.size===0&&Na(Ha),{promise:new Promise(n=>{_r.add(t={c:e,f:n})}),abort(){_r.delete(t)}}}const Ku=/[&"]/g,Ju=/[&<]/g;function Qu(e,t=!1){const n=String(e),r=t?Ku:Ju;r.lastIndex=0;let i="",s=0;for(;r.test(n);){const o=r.lastIndex-1,l=n[o];i+=n.substring(s,o)+(l==="&"?"&":l==='"'?""":"<"),s=o+1}return i+n.substring(s)}function $u(e,t){if(!e||!e.$$render)throw t==="svelte:component"&&(t+=" this={...}"),new Error(`<${t}> is not a valid SSR component. You may need to review your build config to ensure that dependencies are compiled, rather than imported as pre-compiled modules. Otherwise you may need to fix a <${t}>.`);return e}let bs;function La(e){function t(n,r,i,s,o){const l=pu,a={on_destroy:bs,context:new Map(o||(l?l.$$.context:[])),on_mount:[],before_update:[],after_update:[],callbacks:gu()};jo({$$:a});const u=e(n,r,i,s);return jo(l),u}return{render:(n={},{$$slots:r={},context:i=new Map}={})=>{bs=[];const s={title:"",head:"",css:new Set},o=t(s,n,{},r,i);return bt(bs),{html:o,css:{code:Array.from(s.css).map(l=>l.code).join(` +import{y as it,I as bt,J as gu,K as jo,L as pu,M as Ma,s as Xt,l as Se,m as ke,i as le,n as Ge,d as A,e as Ft,z as gt,f as T,g as x,B as be,a as K,h as q,c as J,j as D,k as Ce,D as de,x as w,N as ui,G as _e,O as lt,F as Nt,q as fi,P as mu,Q as Uo,R as _u,S as vu,p as _t,T as ft,U as dt,V as di,W as Pa,X as bu,t as wu,H as It,A as yu,Y as Su}from"../chunks/scheduler.a30ae394.js";import{S as Ut,i as Yt,b as Ye,d as tt,m as Ke,a as xe,t as Ne,e as Je,g as Gt,c as jt,f as zt}from"../chunks/index.49b3fccf.js";import{c as ku,b as wi,e as $r,h as ei,i as Cu,j as We,n as qo,k as Ru,d as Oa,F as Ba,S as pr,g as Eu,m as Wo,o as Au,u as Iu,q as zu,r as vs,s as Fu,t as Du,v as Tu,w as xu,x as Mu,y as Pu,z as Ou,A as Bu,B as Vu,C as Nu,D as Hu,E as Lu,a as Gu,G as ju,H as Uu,I as qu,J as Wu}from"../chunks/stores.6ea4631d.js";/* empty css */import{p as Zu}from"../chunks/stores.b6b25a96.js";import{r as Zo,w as mn,j as Xu,e as _n}from"../chunks/singletons.3d14f100.js";const Va=typeof window<"u";let Xo=Va?()=>window.performance.now():()=>Date.now(),Na=Va?e=>requestAnimationFrame(e):it;const _r=new Set;function Ha(e){_r.forEach(t=>{t.c(e)||(_r.delete(t),t.f())}),_r.size!==0&&Na(Ha)}function Yu(e){let t;return _r.size===0&&Na(Ha),{promise:new Promise(n=>{_r.add(t={c:e,f:n})}),abort(){_r.delete(t)}}}const Ku=/[&"]/g,Ju=/[&<]/g;function Qu(e,t=!1){const n=String(e),r=t?Ku:Ju;r.lastIndex=0;let i="",s=0;for(;r.test(n);){const o=r.lastIndex-1,l=n[o];i+=n.substring(s,o)+(l==="&"?"&":l==='"'?""":"<"),s=o+1}return i+n.substring(s)}function $u(e,t){if(!e||!e.$$render)throw t==="svelte:component"&&(t+=" this={...}"),new Error(`<${t}> is not a valid SSR component. You may need to review your build config to ensure that dependencies are compiled, rather than imported as pre-compiled modules. Otherwise you may need to fix a <${t}>.`);return e}let bs;function La(e){function t(n,r,i,s,o){const l=pu,a={on_destroy:bs,context:new Map(o||(l?l.$$.context:[])),on_mount:[],before_update:[],after_update:[],callbacks:gu()};jo({$$:a});const u=e(n,r,i,s);return jo(l),u}return{render:(n={},{$$slots:r={},context:i=new Map}={})=>{bs=[];const s={title:"",head:"",css:new Set},o=t(s,n,{},r,i);return bt(bs),{html:o,css:{code:Array.from(s.css).map(l=>l.code).join(` `),map:null},head:s.title+s.head}},$$render:t}}async function ef(){const e=["source","id","name","ngenes_input","ngenes","ngenes_signif","genes","genes_signif","pvalue","pvalue_adjust","signif","score_type"],t=Ma(wi);if(Array.isArray(t.genesets)){const n=t.genelist.map(o=>({gene:o.gene,symbol:o.symbol,maxscore:o.sort_score}));n.sort((o,l)=>l.maxscore-o.maxscore);let r=[],i=[];return t.genesets.forEach(o=>{const l=o.genesets.map(d=>{const h=new Set(d.genes),g=new Set(d.genes_signif);return[o.source,d.id,d.name,d.ngenes_input,d.ngenes,d.ngenes_signif,n.filter(f=>h.has(f.gene)).slice(0,250).map(f=>f.symbol).join(","),n.filter(f=>g.has(f.gene)).slice(0,250).map(f=>f.symbol).join(","),d.pvalue,d.pvalue_adjust,d.signif,d.score_type]}),a=r.length,u=o.genesets.map((d,h)=>({i:a+h,pvalue:d.pvalue}));r=r.concat(l),i=i.concat(u)}),i.sort((o,l)=>o.pvalue-l.pvalue),r=i.map(o=>r[o.i]),r.unshift(e),await ku(r)}else return new Blob(["no results available"])}function tf(e,t,n,r){const i=t.genesets.map(o=>o.source);let s=`Geneset analyses GOAT [doi:10.1101/2023.12.10.570979] online (version `+n+" , http://ftwkoopmans.github.io/goat ) was used to perform geneset enrichment analyses";return t.type==="go"?s+=" using genesets from the Gene Ontology database [PMID:10802651] (version "+t.genesets[0].source_version+").":t.type==="syngo"?s+=" using genesets from the SynGO knowledgebase [PMID:31171447] (version "+t.genesets[0].source_version+"). ":s+=' using "'+t.genesets[0].source_version+'" genesets imported into GOAT online in GMT format. ',s+="The input genelist contained "+e.genelist.length+" genes and its "+t.settings.scoreType+"-derived gene scores were used to test for enriched genesets that contained at least "+t.settings.minSize+" and at most "+t.settings.maxSize+" genes (or 50% of the genelist, whichever was smaller) that overlapped with the input genelist. Multiple testing correction was ",i.length>1?s+='independently applied per geneset "source" (i.e. '+i.join(", ")+")":s+="applied",t.settings.pvalueAdjustment=="bonferroni"?s+=" using Bonferroni adjustment":s+=" using the Benjamini-Hochberg procedure (FDR)",i.length>1?s+=" and subsequently all p-values were adjusted (again) using Bonferroni adjustment to account for "+i.length+' separate tests across "sources". ':s+=". ",s+="The significance threshold for adjusted p-values was set to "+t.settings.pvalueThreshold+`. diff --git a/_app/immutable/nodes/5.4e61c7dc.js.br b/_app/immutable/nodes/5.4e61c7dc.js.br new file mode 100644 index 0000000..c44a087 Binary files /dev/null and b/_app/immutable/nodes/5.4e61c7dc.js.br differ diff --git a/_app/immutable/nodes/5.4e61c7dc.js.gz b/_app/immutable/nodes/5.4e61c7dc.js.gz new file mode 100644 index 0000000..9af2354 Binary files /dev/null and b/_app/immutable/nodes/5.4e61c7dc.js.gz differ diff --git a/_app/immutable/nodes/5.57e59d04.js.br b/_app/immutable/nodes/5.57e59d04.js.br deleted file mode 100644 index 93f055f..0000000 Binary files a/_app/immutable/nodes/5.57e59d04.js.br and /dev/null differ diff --git a/_app/immutable/nodes/5.57e59d04.js.gz b/_app/immutable/nodes/5.57e59d04.js.gz deleted file mode 100644 index 1981b7d..0000000 Binary files a/_app/immutable/nodes/5.57e59d04.js.gz and /dev/null differ diff --git a/_app/version.json b/_app/version.json index ee1af99..7173cbc 100644 --- a/_app/version.json +++ b/_app/version.json @@ -1 +1 @@ -{"version":"1702395077818"} \ No newline at end of file +{"version":"1702397704286"} \ No newline at end of file diff --git a/_app/version.json.br b/_app/version.json.br index 4ea7445..c81ee56 100644 Binary files a/_app/version.json.br and b/_app/version.json.br differ diff --git a/_app/version.json.gz b/_app/version.json.gz index b7b79a4..1233358 100644 Binary files a/_app/version.json.gz and b/_app/version.json.gz differ diff --git a/docs.html b/docs.html index cf8e247..f63e131 100644 --- a/docs.html +++ b/docs.html @@ -15,14 +15,14 @@ - + - - + + - - GOAT: Geneset Ordinal Association Test - documentation + + GOAT: Geneset Ordinal Association Test - documentation @@ -72,7 +72,7 @@