diff --git a/docs/index.Rmd b/docs/index.Rmd index 5bdc552..ff1338d 100644 --- a/docs/index.Rmd +++ b/docs/index.Rmd @@ -116,9 +116,9 @@ datatable(dat, extensions = c('Buttons', 'FixedColumns', 'FixedHeader', 'ColReor formatStyle(c("Database"), backgroundColor = '#d6edff') %>% formatStyle(c("Current status"), - backgroundColor = styleEqual(c("Active", "Non-active"), c('#d6edff', 'gray'), default = '#d6edff')) %>% + backgroundColor = styleEqual(c("Active", "Non-active"), c('#d6edff', '#d3d3d3'), default = '#d6edff'), color = "black") %>% formatStyle(c("Last updated"), - backgroundColor = styleEqual(c(NA, ""), c('gray', 'gray'), default = '#d6edff')) + backgroundColor = styleEqual(c(NA, "NA"), c('#d3d3d3', '#d3d3d3'), default = '#d6edff'), color = "black") ``` <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.12.1/css/jquery.dataTables.css"> diff --git a/docs/index.html b/docs/index.html index 733f5f2..c231134 100644 --- a/docs/index.html +++ b/docs/index.html @@ -3436,8 +3436,8 @@ <h1 class="title toc-ignore">Amyloid databases list</h1> <h2 class="tabset"></h2> <div id="amyloid-related-database-list" class="section level3"> <h3>Amyloid-related database list</h3> -<div class="datatables html-widget html-fill-item" id="htmlwidget-21f047951e4975276148" style="width:100%;height:auto;"></div> -<script type="application/json" data-for="htmlwidget-21f047951e4975276148">{"x":{"style":"bootstrap","filter":"top","vertical":false,"filterHTML":"<tr>\n <td data-type=\"character\" style=\"vertical-align: top;\">\n <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n <\/div>\n <\/td>\n <td data-type=\"factor\" style=\"vertical-align: top;\">\n <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n <\/div>\n <div style=\"width: 100%; display: none;\">\n <select multiple=\"multiple\" style=\"width: 100%;\" data-options=\"["Amyloids","IDP regions","Interactions","Prion"]\"><\/select>\n <\/div>\n <\/td>\n <td data-type=\"factor\" style=\"vertical-align: top;\">\n <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n <\/div>\n <div style=\"width: 100%; display: none;\">\n <select multiple=\"multiple\" style=\"width: 100%;\" data-options=\"["Experimental","Experimental and prediction","Prediction"]\"><\/select>\n <\/div>\n <\/td>\n <td data-type=\"factor\" style=\"vertical-align: top;\">\n <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n 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href='http://comprec-lin.iiar.pwr.edu.pl/amyload/' target='_blank'>AmyLoad<\/a>","<a href='https://amyloid.cs.mcgill.ca/database/index.html' target='_blank'>Fibrilizer<\/a>","<a href='https://services.mbi.ucla.edu/zipperdb/intro' target='_blank'>ZipperDB<\/a>","<a href='https://pedb.vib.be/' target='_blank'>pE-DB<\/a>","<a href='https://amypdb.univ-rennes1.fr/' target='_blank'>AmyPDB<\/a>","<a href='http://bicmku.in/ProADD' target='_blank'>ProADD<\/a>","<a href='http://bioinformatics.biol.uoa.gr/amyco' target='_blank'>AmyCo<\/a>","<a href='http://www.bioinformatics.leeds.ac.uk/group/online/fibril_one' target='_blank'>fibril_one<\/a>","<a href='http://83.212.109.111/amyloid_interactome' target='_blank'>amyloid interactome<\/a>","<a href='https://libaio.biol.mcgill.ca/prion' target='_blank'>PrionHome<\/a>","<a href='http://www.nih.go.kr/therpa' target='_blank'>THERPA<\/a>","<a href='http://prion.systemsbiology.net' target='_blank'>The Prion Disease Database<\/a>"],["Amyloids","Amyloids","Amyloids","Amyloids","IDP regions","Amyloids","Interactions","Amyloids","Amyloids","Prion","Amyloids","Amyloids","Amyloids",null,null,null,null,null,null,"Prion",null,"Prion"],["Experimental","Experimental","Experimental and prediction","Experimental","Prediction","Experimental","Experimental","Experimental and prediction","Experimental and prediction","Prediction","Experimental and prediction","Prediction","Prediction",null,null,null,null,null,null,"Experimental and 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PubMed","PDB",null,null,null,null,null,null,null,null,null,null],["<a href='https://doi.org/10.1038%2Fembor.2011.116' target='_blank'>10.1038%2Fembor.2011.116<\/a>","<a href='https://doi.org/10.1016/j.cell.2021.08.013' target='_blank'>10.1016/j.cell.2021.08.013<\/a>","<a href='https://doi.org/10.1101/2024.02.12.579644' target='_blank'>10.1101/2024.02.12.579644<\/a>","<a href='https://doi.org/10.1080/13506129.2020.1715363' target='_blank'>10.1080/13506129.2020.1715363<\/a>","<a href='https://doi.org/10.3389/fmolb.2022.882160' target='_blank'>10.3389/fmolb.2022.882160<\/a>","<a href='https://doi.org/10.1093/nar/gkx950' target='_blank'>10.1093/nar/gkx950<\/a>","<a href='https://doi.org/10.1093/nar/gkac882' target='_blank'>10.1093/nar/gkac882<\/a>","<a href='https://doi.org/10.1093/bioinformatics/btac126' target='_blank'>10.1093/bioinformatics/btac126<\/a>","<a href='https://doi.org/10.1093/nar/gkz758' target='_blank'>10.1093/nar/gkz758<\/a>","<a href='https://doi.org/10.1186/1471-2164-15-102' target='_blank'>10.1186/1471-2164-15-102<\/a>","<a href='https://doi.org/10.1093/bioinformatics/btv375' target='_blank'>10.1093/bioinformatics/btv375<\/a>","<a href='http://dx.doi.org/10.1016/j.bpj.2012.12.037' target='_blank'>10.1016/j.bpj.2012.12.037<\/a>","<a href='https://doi.org/10.1073/pnas.0915166107' target='_blank'>10.1073/pnas.0915166107<\/a>","<a href='https://doi.org/10.1093/nar/gkt960' target='_blank'>10.1093/nar/gkt960<\/a>","<a href='https://doi.org/10.1186/1471-2105-9-273' target='_blank'>10.1186/1471-2105-9-273<\/a>","<a href='https://doi.org/10.6026%2F97320630010390' target='_blank'>10.6026%2F97320630010390<\/a>","<a href='https://doi.org/10.1080/13506129.2019.1603143' target='_blank'>10.1080/13506129.2019.1603143<\/a>","<a href='https://doi.org/10.1110%2Fps.0204302' target='_blank'>10.1110%2Fps.0204302<\/a>","<a href='https://doi.org/10.1371/journal.pone.0173163' target='_blank'>10.1371/journal.pone.0173163<\/a>","<a href='https://doi.org/10.1371/journal.pone.0031785' target='_blank'>10.1371/journal.pone.0031785<\/a>","<a href='http://dx.doi.org/10.1080/19336896.2019.1689789' target='_blank'>10.1080/19336896.2019.1689789<\/a>","<a href='https://doi.org/10.1093/database/bap011' target='_blank'>10.1093/database/bap011<\/a>"]],"container":"<table class=\"table table-striped table-hover row-border order-column display\">\n <thead>\n <tr>\n <th>Database<\/th>\n <th>Focus<\/th>\n <th>Type of data<\/th>\n <th>Only amyloids<\/th>\n <th>Includes experimental conditions<\/th>\n <th>Usability<\/th>\n <th>Includes structural information<\/th>\n <th>Identifies APRs<\/th>\n <th>Current status<\/th>\n <th>Last updated<\/th>\n <th>Data sources and links to other db<\/th>\n <th>DOI<\/th>\n <\/tr>\n 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<\/td>\n <td data-type=\"character\" style=\"vertical-align: top;\">\n <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n <\/div>\n <\/td>\n<\/tr>","extensions":["Buttons","FixedColumns","FixedHeader","ColReorder","KeyTable"],"data":[["<a href='http://bioserver2.sbsc.unifi.it/AmyloBase.html' target='_blank'>AmyloBase<\/a>","<a href='https://people.mbi.ucla.edu/sawaya/amyloidatlas/' target='_blank'>Amyloid Atlas<\/a>","<a href='https://crossbetadb.crbm.cnrs.fr/' target='_blank'>Cross-Beta DB<\/a>","<a href='https://web.iitm.ac.in/bioinfo2/cpad2/index.html' target='_blank'>CPAD2<\/a>","<a href='http://carsdb.ppmclab.com/' target='_blank'>CARs DB<\/a>","<a href='http://amypro.net' target='_blank'>AmyPro<\/a>","<a href='http://amylograph.com/' target='_blank'>AmyloGraph<\/a>","<a href='https://stamp.switchlab.org/' target='_blank'>StAmP<\/a>","<a href='http://waltzdb.switchlab.org/' target='_blank'>Waltz DB 2.0<\/a>","<a href='http://www.nih.go.kr/therpa' target='_blank'>THERPA<\/a>","<a href='http://webapps.bifi.es/prionscan' target='_blank'>PrionScan<\/a>","<a href='http://bioinformatics.biol.uoa.gr/amyco' target='_blank'>AmyCo<\/a>","<a href='http://83.212.109.111/amyloid_interactome' target='_blank'>amyloid interactome<\/a>","<a href='http://comprec-lin.iiar.pwr.edu.pl/amyload/' target='_blank'>AmyLoad<\/a>","<a href='http://bicmku.in/ProADD' target='_blank'>ProADD<\/a>","<a href='https://pedb.vib.be/' target='_blank'>pE-DB<\/a>","<a href='https://amyloid.cs.mcgill.ca/database/index.html' target='_blank'>Fibrilizer<\/a>","<a href='https://libaio.biol.mcgill.ca/prion' target='_blank'>PrionHome<\/a>","<a href='https://services.mbi.ucla.edu/zipperdb/intro' target='_blank'>ZipperDB<\/a>","<a href='http://prion.systemsbiology.net' target='_blank'>The Prion Disease Database<\/a>","<a href='http://www.bioinformatics.leeds.ac.uk/group/online/fibril_one' target='_blank'>fibril_one<\/a>","<a href='https://amypdb.univ-rennes1.fr/' target='_blank'>AmyPDB<\/a>"],["Amyloids","Amyloids","Amyloids","Amyloids","IDP regions","Amyloids","Interactions","Amyloids","Amyloids","Prion","Prion","Amyloids","Interactions","Amyloids","Amyloids","Structural","Amyloids","Prion","Amyloids","Prion","Amyloids","Amyloids"],["Experimental","Experimental","Experimental and prediction","Experimental","Prediction","Experimental","Experimental","Experimental and prediction","Experimental and prediction",null,"Prediction",null,null,"Experimental and prediction",null,null,"Prediction","Experimental and prediction","Prediction","Experimental",null,null],["Yes","Yes","Yes","No","Yes","No","Yes","Yes","No",null,"Yes",null,null,"No",null,null,"Yes",null,null,null,null,null],["Yes","No","Yes","Yes","No","No","No","No","Yes",null,"No",null,null,"Yes",null,null,"No","Yes","No","Yes",null,null],["General","General","General","General","General","General","General","Specific","General",null,"General",null,null,"General",null,null,"Specific","General","General","Specific",null,null],["Sequence-only","Structure for the wt protein and the aggregate","Structure for the wt protein","Structure for the wt protein","Sequence-only","Structure for the wt protein","Sequence-only","Sequence-only","Structure for the wt protein and the aggregate",null,"Sequence-only",null,null,"Sequence-only",null,null,"Structure for the wt protein","Structure for the wt protein","Structure for the wt protein and the aggregate","Sequence-only",null,null],["No","No","APRs","APRs","APRs","APRs","No","APRs","APRs",null,"APRs",null,null,"No",null,null,"No","No","APRs","No",null,null],["Active","Active","Active","Active","Active","Active","Active","Active","Active","Non-active","Active","Non-active","Non-active","Active","Non-active","Non-active","Active","Non-active","Non-active","Non-active","Non-active","Non-active"],["2024-07-12","2024-05-22","2024-05-01","2024-04-15","2023-09-08","2023-08-25","2023-06-08","2022-03-09","2020-01-08","2019-10-25","2019-07-03","2019-05-16","2017-03-01","2015-06-17","2014-06-30","2014-01-01","2013-02-05","2012-02-20","2010-02-03","2009-09-17","2009-04-13","2008-06-10"],["PubMed; UniProt","PDB; PubMed","PDB; AmyPro; UniProt; PubMed","CPAD; Waltz-DB 2.0; AmyLoad; AmyPro; UniProt; PDB; PubMed","DisProt; UniProt","PDB; UniProt; PubMed","PubMed; UniProt","WALTZ-DB; AmyPro; CPAD; PDB; UniProt","PubMed; UniProt; PDB",null,"UniProt; ENA; Protein; KEGG; Pfam; QuickGO",null,null,"TANGO; WALTZ; AmylFrag; AGGRESCAN; AmylHex; PubMed",null,null,"PDB",null,null,null,null,null],["<a href='https://doi.org/10.1038%2Fembor.2011.116' target='_blank'>10.1038%2Fembor.2011.116<\/a>","<a href='https://doi.org/10.1016/j.cell.2021.08.013' target='_blank'>10.1016/j.cell.2021.08.013<\/a>","<a href='https://doi.org/10.1101/2024.02.12.579644' target='_blank'>10.1101/2024.02.12.579644<\/a>","<a href='https://doi.org/10.1080/13506129.2020.1715363' target='_blank'>10.1080/13506129.2020.1715363<\/a>","<a href='https://doi.org/10.3389/fmolb.2022.882160' target='_blank'>10.3389/fmolb.2022.882160<\/a>","<a href='https://doi.org/10.1093/nar/gkx950' target='_blank'>10.1093/nar/gkx950<\/a>","<a href='https://doi.org/10.1093/nar/gkac882' target='_blank'>10.1093/nar/gkac882<\/a>","<a href='https://doi.org/10.1093/bioinformatics/btac126' target='_blank'>10.1093/bioinformatics/btac126<\/a>","<a href='https://doi.org/10.1093/nar/gkz758' target='_blank'>10.1093/nar/gkz758<\/a>","<a href='http://dx.doi.org/10.1080/19336896.2019.1689789' target='_blank'>10.1080/19336896.2019.1689789<\/a>","<a href='https://doi.org/10.1186/1471-2164-15-102' target='_blank'>10.1186/1471-2164-15-102<\/a>","<a href='https://doi.org/10.1080/13506129.2019.1603143' target='_blank'>10.1080/13506129.2019.1603143<\/a>","<a href='https://doi.org/10.1371/journal.pone.0173163' target='_blank'>10.1371/journal.pone.0173163<\/a>","<a href='https://doi.org/10.1093/bioinformatics/btv375' target='_blank'>10.1093/bioinformatics/btv375<\/a>","<a href='https://doi.org/10.6026%2F97320630010390' target='_blank'>10.6026%2F97320630010390<\/a>","<a href='https://doi.org/10.1093/nar/gkt960' target='_blank'>10.1093/nar/gkt960<\/a>","<a href='http://dx.doi.org/10.1016/j.bpj.2012.12.037' target='_blank'>10.1016/j.bpj.2012.12.037<\/a>","<a href='https://doi.org/10.1371/journal.pone.0031785' target='_blank'>10.1371/journal.pone.0031785<\/a>","<a href='https://doi.org/10.1073/pnas.0915166107' target='_blank'>10.1073/pnas.0915166107<\/a>","<a href='https://doi.org/10.1093/database/bap011' target='_blank'>10.1093/database/bap011<\/a>","<a href='https://doi.org/10.1110%2Fps.0204302' target='_blank'>10.1110%2Fps.0204302<\/a>","<a href='https://doi.org/10.1186/1471-2105-9-273' target='_blank'>10.1186/1471-2105-9-273<\/a>"]],"container":"<table class=\"table table-striped table-hover row-border order-column display\">\n <thead>\n <tr>\n <th>Database<\/th>\n <th>Focus<\/th>\n <th>Type of data<\/th>\n <th>Only amyloids<\/th>\n <th>Includes experimental conditions<\/th>\n <th>Usability<\/th>\n <th>Includes structural information<\/th>\n <th>Identifies APRs<\/th>\n <th>Current status<\/th>\n <th>Last updated<\/th>\n <th>Data sources and links to other db<\/th>\n <th>DOI<\/th>\n <\/tr>\n 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