{"id":67,"date":"2022-01-31T15:34:37","date_gmt":"2022-01-31T21:34:37","guid":{"rendered":"http:\/\/victortrevino.bioinformatics.mx\/?page_id=67"},"modified":"2025-05-05T08:16:55","modified_gmt":"2025-05-05T14:16:55","slug":"bioinfo-tools","status":"publish","type":"page","link":"https:\/\/victortrevino.bioinformatics.mx\/index.php\/bioinfo-tools\/","title":{"rendered":"Bioinfo-Tools"},"content":{"rendered":"\n<p><a href=\"https:\/\/bioinformatics.mx\/app\/ALLeQTL\/eQTLgene.jsp?gene=TP53\">ALLeQTLs : cis-eQTLs from GTEx data (Farid Jacome&#8217;s Thesis)<\/a><\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"678\" src=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/10\/eQTLs-1-1024x678.png\" alt=\"\" class=\"wp-image-166\" srcset=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/10\/eQTLs-1-1024x678.png 1024w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/10\/eQTLs-1-300x199.png 300w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/10\/eQTLs-1-768x508.png 768w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/10\/eQTLs-1.png 1506w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<p><span style=\"text-decoration: underline;\"><a href=\"https:\/\/bioinformatics.mx\/app\/cogtex2\/geneinput.jsp?gene=BRCA2\">CoGTex-2 : Views of Co-Expression from GTeX data<\/a> (Maria Julia Teja<\/span>)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"1023\" height=\"554\" src=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/07\/image.png\" alt=\"\" class=\"wp-image-152\" srcset=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/07\/image.png 1023w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/07\/image-300x162.png 300w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/07\/image-768x416.png 768w\" sizes=\"auto, (max-width: 1023px) 100vw, 1023px\" \/><\/figure>\n\n\n\n<p><a href=\"https:\/\/bioinformatics.mx\/app\/cogtex\" target=\"_blank\" rel=\"noreferrer noopener\">CoGTex: A Co-Expression Platform from GTeX data (Miguel Cortes Thesis).<\/a> Paper on <em><a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0309961\">PLoS One<\/a><\/em><\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><a href=\"https:\/\/victortrevino.bioinformatics.mx\/cogtex\"><img loading=\"lazy\" decoding=\"async\" width=\"916\" height=\"655\" src=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/CoGTex.jpg\" alt=\"\" class=\"wp-image-93\" style=\"width:607px;height:434px\" srcset=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/CoGTex.jpg 916w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/CoGTex-300x215.jpg 300w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/CoGTex-768x549.jpg 768w\" sizes=\"auto, (max-width: 916px) 100vw, 916px\" \/><\/a><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-css-opacity\"\/>\n\n\n\n<p><a href=\"http:\/\/bioinformatics.mx\/SurvHotspots\" target=\"_blank\" rel=\"noreferrer noopener\">SurvHotspots: An informative database for survival analysis of cancer hotspots (Melissa Gonzalez Thesis).<\/a> Paper on <em><a href=\"https:\/\/www.mdpi.com\/2072-6694\/16\/5\/1072\">Cancers<\/a><\/em><\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><a href=\"http:\/\/bioinformatics.mx\/SurvHotspots\"><img loading=\"lazy\" decoding=\"async\" width=\"612\" height=\"520\" src=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2023\/07\/SurvHotspots-v2.png\" alt=\"\" class=\"wp-image-130\" srcset=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2023\/07\/SurvHotspots-v2.png 612w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2023\/07\/SurvHotspots-v2-300x255.png 300w\" sizes=\"auto, (max-width: 612px) 100vw, 612px\" \/><\/a><\/figure>\n\n\n\n<figure class=\"wp-block-image size-large is-resized\"><a href=\"http:\/\/bioinformatics.mx\/SurvHotspots-vMely\/index.php\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"763\" src=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/06\/SurvHotspots-1024x763.png\" alt=\"\" class=\"wp-image-120\" style=\"width:276px;height:204px\" srcset=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/06\/SurvHotspots-1024x763.png 1024w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/06\/SurvHotspots-300x224.png 300w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/06\/SurvHotspots-768x572.png 768w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/06\/SurvHotspots.png 1323w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/a><figcaption class=\"wp-element-caption\">Melissa&#8217;s Thesis Version<\/figcaption><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<p><a href=\"https:\/\/victortrevino.bioinformatics.mx:8181\/Biomatec\/pubterm.html\" target=\"_blank\" rel=\"noreferrer noopener\">PubTerm: A web-based annotation tool for PubMed articles, genes, or any other biomedical term.<\/a> Paper on <a href=\"https:\/\/academic.oup.com\/database\/article-lookup\/doi\/10.1093\/database\/bay137\">Databases<\/a> (Jos\u00e9 Garcia-Pelaez).<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><a href=\"https:\/\/victortrevino.bioinformatics.mx:8080\/Biomatec\/pubterm.html\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"571\" src=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/Figure5-1024x571.jpg\" alt=\"\" class=\"wp-image-89\" srcset=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/Figure5-1024x571.jpg 1024w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/Figure5-300x167.jpg 300w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/Figure5-768x428.jpg 768w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/Figure5-1536x856.jpg 1536w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/Figure5-2048x1142.jpg 2048w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/Figure5-1568x874.jpg 1568w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/a><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-css-opacity\"\/>\n\n\n\n<p><a href=\"https:\/\/victortrevino.bioinformatics.mx:8181\/Biomatec\/SurvivaX.jsp\" target=\"_blank\" rel=\"noreferrer noopener\">SurvExpress: A web-based analysis of transcriptomic biomarkers in cancer.<\/a> Paper on <a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0074250\" target=\"_blank\" rel=\"noreferrer noopener\">PLOS One (Ra\u00fal Aguirre-Gamboa Thesis).<\/a><\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><a href=\"https:\/\/victortrevino.bioinformatics.mx:8080\/Biomatec\/SurvivaX.jsp\"><img loading=\"lazy\" decoding=\"async\" width=\"381\" height=\"187\" src=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/SurvExpress.jpg\" alt=\"\" class=\"wp-image-90\" style=\"aspect-ratio:2.037974683544304;width:607px;height:auto\" srcset=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/SurvExpress.jpg 381w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/SurvExpress-300x147.jpg 300w\" sizes=\"auto, (max-width: 381px) 100vw, 381px\" \/><\/a><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-css-opacity\"\/>\n\n\n\n<p><a href=\"https:\/\/victortrevino.bioinformatics.mx\/app\/HotSpotsAnnotations\" target=\"_blank\" rel=\"noreferrer noopener\">HotspotsAnnotations: A web-based tool to annotate\/visualize hotspots in cancer.<\/a> Paper on <a href=\"https:\/\/academic.oup.com\/database\/article-lookup\/doi\/10.1093\/database\/baaa025\" target=\"_blank\" rel=\"noreferrer noopener\">Database<\/a>.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><a href=\"https:\/\/victortrevino.bioinformatics.mx:8080\/HotSpotsAnnotations\"><img loading=\"lazy\" decoding=\"async\" width=\"639\" height=\"553\" src=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/HotSpotAnnotations.jpg\" alt=\"\" class=\"wp-image-91\" style=\"aspect-ratio:1.160092807424594;width:592px;height:auto\" srcset=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/HotSpotAnnotations.jpg 639w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/HotSpotAnnotations-300x260.jpg 300w\" sizes=\"auto, (max-width: 639px) 100vw, 639px\" \/><\/a><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-css-opacity\"\/>\n\n\n\n<p>SurvMicro: A web-based analysis of micro RNA expression biomarkers in cancer. (Server down). Paper on <a href=\"https:\/\/academic.oup.com\/bioinformatics\/article-lookup\/doi\/10.1093\/bioinformatics\/btu087\" target=\"_blank\" rel=\"noreferrer noopener\">Bioinformatics<\/a>. (Ra\u00fal Aguirre-Gamboa Thesis)<\/p>\n\n\n\n<hr class=\"wp-block-separator has-css-opacity\"\/>\n\n\n\n<p>GALGO: Genetic Algorithms for Optimization. An R package for generic search optimizations. <a href=\"https:\/\/academic.oup.com\/bioinformatics\/article-lookup\/doi\/10.1093\/bioinformatics\/btl074\" target=\"_blank\" rel=\"noreferrer noopener\">Paper on Bioinformatics<\/a>. <br>See <a href=\"https:\/\/cran.r-project.org\/package=galgo\" target=\"_blank\" rel=\"noreferrer noopener\">Galgo on CRAN R packages<\/a>. Galgo <a href=\"https:\/\/www.dropbox.com\/scl\/fi\/a7hi2g4ljvufintpspm3h\/GALGO-TUTORIAL-1.2.pdf?rlkey=vs1h4kt6w6k0z2xb1zy91ar53&amp;dl=0\" target=\"_blank\" rel=\"noreferrer noopener\">Tutorial<\/a>. <br>Galgo source code on <a href=\"https:\/\/github.com\/vtrevino\/GALGO\" target=\"_blank\" rel=\"noreferrer noopener\">GitHub<\/a><\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"822\" height=\"226\" src=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/03\/image.png\" alt=\"\" class=\"wp-image-134\" srcset=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/03\/image.png 822w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/03\/image-300x82.png 300w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2024\/03\/image-768x211.png 768w\" sizes=\"auto, (max-width: 822px) 100vw, 822px\" \/><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-css-opacity\"\/>\n\n\n\n<p>VALORATE: Velocity and Accuracy of the LOg-RAnk TEst. R package to quickly estimates the distribution of the log-rank especially for heavy unbalanced groups.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>CRAN package: <br><a href=\"https:\/\/cran.r-project.org\/web\/packages\/valorate\/index.html\">https:\/\/cran.r-project.org\/web\/packages\/valorate\/index.html<\/a><\/li>\n\n\n\n<li>Beta\/Early implementation: <br><a href=\"https:\/\/github.com\/vtrevino\/valorate\">https:\/\/github.com\/vtrevino\/valorate<\/a><\/li>\n\n\n\n<li>Package Paper in Bioinformatics (PubMed):<br><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28186225\/\">https:\/\/pubmed.ncbi.nlm.nih.gov\/28186225\/<\/a><\/li>\n\n\n\n<li>Model Paper in Scientific Reports:<br><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/28240231\/\">https:\/\/pubmed.ncbi.nlm.nih.gov\/28240231\/<\/a><\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-image size-large\"><img decoding=\"async\" src=\"https:\/\/media.springernature.com\/lw685\/springer-static\/image\/art%3A10.1038%2Fsrep43350\/MediaObjects\/41598_2017_Article_BFsrep43350_Fig1_HTML.jpg?as=webp\" alt=\"\"\/><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<p>GridMass: A MzMine add-on for peak detection (feature detection) in the analysis of metabolomics data. Paper on <a href=\"https:\/\/doi.org\/10.1002\/jms.3512\" target=\"_blank\" rel=\"noreferrer noopener\">J on Mass Spectometry<\/a>.<br>GridMass on <a href=\"https:\/\/github.com\/mzmine\/mzmine2\/releases\" target=\"_blank\" rel=\"noreferrer noopener\">MZMine 2<\/a>, or <a href=\"http:\/\/mzmine.github.io\/features.html\" target=\"_blank\" rel=\"noreferrer noopener\">MZMine 3<\/a>.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"560\" height=\"676\" src=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/GridMass.jpg\" alt=\"\" class=\"wp-image-92\" style=\"aspect-ratio:0.8278829604130808;width:609px;height:auto\" srcset=\"https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/GridMass.jpg 560w, https:\/\/victortrevino.bioinformatics.mx\/wp-content\/uploads\/2022\/03\/GridMass-249x300.jpg 249w\" sizes=\"auto, (max-width: 560px) 100vw, 560px\" \/><\/figure>\n\n\n\n<hr class=\"wp-block-separator has-css-opacity\"\/>\n\n\n\n<p><strong>PUBTERM CURATED GENE LISTS FROM OUR PUBLICATIONS<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a rel=\"noreferrer noopener\" href=\"\/VitaminD.html\" target=\"_blank\">VitaminD<\/a><\/li>\n\n\n\n<li><a rel=\"noreferrer noopener\" href=\"\/MitoCancer.html\" target=\"_blank\">Mitochondrial Genes in Cancer<\/a><\/li>\n\n\n\n<li><a rel=\"noreferrer noopener\" href=\"\/CrohnDisease.html\" target=\"_blank\">Crohn&#8217;s Disease<\/a><\/li>\n\n\n\n<li><a href=\"\/PAH.html\" target=\"_blank\" rel=\"noreferrer noopener\">Pulmonary Arterial Hypertension<\/a><\/li>\n<\/ul>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>ALLeQTLs : cis-eQTLs from GTEx data (Farid Jacome&#8217;s Thesis) CoGTex-2 : Views of Co-Expression from GTeX data (Maria Julia Teja) CoGTex: A Co-Expression Platform from GTeX data (Miguel Cortes Thesis). Paper on PLoS One SurvHotspots: An informative database for survival analysis of cancer hotspots (Melissa Gonzalez Thesis). Paper on Cancers PubTerm: A web-based annotation tool&hellip; <a class=\"more-link\" href=\"https:\/\/victortrevino.bioinformatics.mx\/index.php\/bioinfo-tools\/\">Continue reading <span class=\"screen-reader-text\">Bioinfo-Tools<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-67","page","type-page","status-publish","hentry","entry"],"_links":{"self":[{"href":"https:\/\/victortrevino.bioinformatics.mx\/index.php\/wp-json\/wp\/v2\/pages\/67","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/victortrevino.bioinformatics.mx\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/victortrevino.bioinformatics.mx\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/victortrevino.bioinformatics.mx\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/victortrevino.bioinformatics.mx\/index.php\/wp-json\/wp\/v2\/comments?post=67"}],"version-history":[{"count":34,"href":"https:\/\/victortrevino.bioinformatics.mx\/index.php\/wp-json\/wp\/v2\/pages\/67\/revisions"}],"predecessor-version":[{"id":181,"href":"https:\/\/victortrevino.bioinformatics.mx\/index.php\/wp-json\/wp\/v2\/pages\/67\/revisions\/181"}],"wp:attachment":[{"href":"https:\/\/victortrevino.bioinformatics.mx\/index.php\/wp-json\/wp\/v2\/media?parent=67"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}