{"id":244,"date":"2018-03-26T20:03:40","date_gmt":"2018-03-26T12:03:40","guid":{"rendered":"http:\/\/www.gao-lab.org\/?page_id=244"},"modified":"2024-02-24T23:09:04","modified_gmt":"2024-02-24T15:09:04","slug":"data-and-tools-2","status":"publish","type":"page","link":"https:\/\/www.gao-lab.org\/index.php\/data-and-tools-2\/","title":{"rendered":"Data and Tools"},"content":{"rendered":"<p>All these resources below are publicly available for researchers around the world. Feel free to <a href=\"http:\/\/www.gao-lab.org\/index.php\/en\/contact-2\/\">contact us<\/a> for questions\/issues\/comments.<\/p>\n<ul>\n<li id=\"cblast\"><a href=\"https:\/\/cblast.gao-lab.org\">Cell BLAST<\/a>: a large-scale integration &#038; searching algorithm for massive heterogeneous scRNA-seq data.<\/li>\n<li id=\"glue\"><a href=\"https:\/\/github.com\/gao-lab\/GLUE\">GLUE\/CLUE<\/a> for multi-omics integration and regulatory inference.<\/li>\n<li id=\"slat\"><a href=\"https:\/\/github.com\/gao-lab\/SLAT\">SLAT<\/a> for aligning heterogeneous spatial slices across various conditions, platforms as well as modalities.<\/li>\n<\/ul>\n<ul>\n<li id=\"locexpress\"><a href=\"http:\/\/loc-express.gao-lab.org\">LocExpress<\/a>: estimating expression of novel transcripts across multiple tissues and cell types in real time.<\/li>\n<li id=\"cpc\"><a href=\"http:\/\/cpc2.gao-lab.org\">CPC2<\/a>: Coding Potential Calculator, version 2, the <a href=\"http:\/\/cpc.gao-lab.org\">CPC1<\/a> is also available.<\/li>\n<li id=\"ribocalc\"><a href=\"https:\/\/github.com\/gao-lab\/RiboCalc\">RibpCalc<\/a>: Modeling RNA Coding Ability quantitatively.<\/li>\n<li id=\"annolnc\"><a href=\"http:\/\/annolnc.gao-lab.org\">AnnoLnc<\/a>: on-the-fly analysis for novel human long noncoding RNAs(lncRNAs).<\/li>\n<li id=\"reflnc\"><a href=\"http:\/\/reflnc.gao-lab.org\">RefLnc<\/a>: a comprehensive annotation for human long noncoding RNAs(lncRNAs).<\/li>\n<li id=\"lost_and_found\"><a href=\"https:\/\/github.com\/gao-lab\/LOST_and_FOUND\">LOST &#038; FOUND<\/a> for calling loss events for protein-coding genes.<\/li>\n<\/ul>\n<ul>\n<li id=\"cope\"><a href=\"http:\/\/cope.gao-lab.org\">COPE<\/a> \uff1athe first context-sensitive variant annotation tool for <a href=\"http:\/\/cope.gao-lab.org\/run_PCG.html\">coding variants<\/a> and <a href=\"http:\/\/cope.gao-lab.org\/run_TFBS.html\">regulatory variants at TFBS.<\/a><\/li>\n<li id=\"carmen\"><a href=\"http:\/\/carmen.gao-lab.org\/\">CARMEN<\/a>: a novel algorithm to identify functional noncoding expression-modulating variants.<\/li>\n<li id=\"reva\"><a href=\"http:\/\/reva.gao-lab.org\/\">REVA<\/a>: a database for noncoding expression-modulating variant.<\/li>\n<li id=\"esccdb\"><a href=\"http:\/\/esccdb.gao-lab.org\">CCGD\/ESCC<\/a>: Chinese Cancer Genomic Database-Esophageal Squamous-Cell Carcinoma, a joint work with <a href=\"http:\/\/pumc.teacher.360eol.com\/teacherBasic\/preview?teacherId=4142\">Wu Lab at State Key Laboratory of Molecular Oncology, Chinese Academy of Medical Science<\/a><\/li>\n<\/ul>\n<ul>\n<li id=\"planttfdb\"><a href=\"http:\/\/planttfdb.gao-lab.org\">PlantTFDB<\/a> : Plant Transcription Factor Database, a portal for the functional and evolutionary study of plant transcription factors.<\/li>\n<li id=\"plantregmap\"><a href=\"http:\/\/plantregmap.gao-lab.org\">PlantRegMap<\/a> : a portal for the regulation data and analysis tools in plants.<\/li>\n<li id=\"atrm\"><a href=\"http:\/\/atrm.gao-lab.org\/\">ATRM<\/a>: a database for Arabidopsis transcriptional regulatory map.<\/li>\n<\/ul>\n<p>Meanwhile, we also make several powerful <strong>computing and data integrating infrastructures<\/strong> we developed freely available to the community, as both open source toolkit and public Webserver.<\/p>\n<ul>\n<li id=\"gsds\"><a href=\"http:\/\/gsds.gao-lab.org\">GSDS<\/a>: a gene feature visualization server.<\/li>\n<li id=\"weblab\"><a href=\"http:\/\/weblab.gao-lab.org\">WebLab<\/a>: a multifunctional bioinformatics analysis platform integrating diversified tools with unified, user-friendly web interface.<\/li>\n<li id=\"abrowse\"><a href=\"http:\/\/abrowse.gao-lab.org\">ABrowse<\/a>: a customizable next-generation genome browser framework.<\/li>\n<li id=\"abcgrid\"><a href=\"http:\/\/abcgrid.cbi.pku.edu.cn\">ABCGrid<\/a>: a Java-based lightweight Application of Bioinformatics Computing Grid<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>All these resources below are publicly available for researchers around the world. Feel free to contact us for questions\/issues\/comments. Cell BLAST: a large-scale integration &#038; searching algorithm for massive heterogeneous scRNA-seq data. GLUE\/CLUE for multi-omics integration and regulatory inference. SLAT for aligning heterogeneous spatial slices across various conditions, platforms as well as modalities. LocExpress: estimating <a href=\"https:\/\/www.gao-lab.org\/index.php\/data-and-tools-2\/\" rel=\"nofollow\"><span class=\"sr-only\">Read more about Data and Tools<\/span>[&hellip;]<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-244","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.gao-lab.org\/index.php\/wp-json\/wp\/v2\/pages\/244","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.gao-lab.org\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.gao-lab.org\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.gao-lab.org\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.gao-lab.org\/index.php\/wp-json\/wp\/v2\/comments?post=244"}],"version-history":[{"count":30,"href":"https:\/\/www.gao-lab.org\/index.php\/wp-json\/wp\/v2\/pages\/244\/revisions"}],"predecessor-version":[{"id":1515,"href":"https:\/\/www.gao-lab.org\/index.php\/wp-json\/wp\/v2\/pages\/244\/revisions\/1515"}],"wp:attachment":[{"href":"https:\/\/www.gao-lab.org\/index.php\/wp-json\/wp\/v2\/media?parent=244"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}