{"id":26,"date":"2016-05-22T20:55:03","date_gmt":"2016-05-22T20:55:03","guid":{"rendered":"https:\/\/jira-test.ki.se\/wpsites\/truvu\/?page_id=26"},"modified":"2026-01-16T17:10:38","modified_gmt":"2026-01-16T17:10:38","slug":"bioinformatics-tools","status":"publish","type":"page","link":"https:\/\/www.meb.ki.se\/sites\/truvu\/bioinformatics-tools\/","title":{"rendered":"Bioinformatics tools"},"content":{"rendered":"<p>I have developed (co-developed) the following bioinformatics tools:<\/p>\n<ul>\n<li><strong><a href=\"https:\/\/github.com\/Qingyueee\/SR2P\">SR2P<\/a><\/strong>: Predicting spatial protein abundance from gene expression in spatial transcriptomics data<\/li>\n<li><a href=\"https:\/\/github.com\/thng4165\/Drug-Repurposing\"><strong>NMF-PDR<\/strong><\/a>: Permutation-based Non-negative Matrix Factorization approach for drug repurposing<\/li>\n<li><a href=\"https:\/\/github.com\/Qingyueee\/DECLUST\"><strong>DECLUST<\/strong><\/a>: A cluster-based cell-type deconvolution of spatial transcriptomic data<\/li>\n<li><a href=\"https:\/\/www.meb.ki.se\/shiny\/truvu\/MUSEC\/\"><strong>MUSEC<\/strong><\/a>: Mutant-allele Isoform Explorer for cancers<\/li>\n<li><a href=\"https:\/\/github.com\/nghiavtr\/MegaFun\"><strong>MegaFun<\/strong><\/a>: Functional quantification of microbiome from metagenomics<\/li>\n<li><a href=\"https:\/\/github.com\/tracquangthinh\/DIPx\"><strong>DIPx:<\/strong><\/a>\u00a0Pathway activation model for personalized prediction of drug synergy<\/li>\n<li><a href=\"https:\/\/www.meb.ki.se\/shiny\/truvu\/MDREAM\/\"><strong>MDREAM<\/strong><\/a>: A web-based tool of\u00a0Monotherapy Drug Response prediction for acute myeloid leukemia patients<\/li>\n<li><a href=\"https:\/\/github.com\/nghiavtr\/FuSeq_WES\"><strong>FuSeq_WES<\/strong><\/a>: A method for detection of fusion genes from DNA-sequencing data<\/li>\n<li><a href=\"https:\/\/www.meb.ki.se\/shiny\/truvu\/DCSP\/\"><strong>DCSP<\/strong><\/a>: Discovery of Druggable Cancer-Specific Pathways<\/li>\n<li><a href=\"https:\/\/github.com\/wenjiangdeng\/MAX\"><strong>MAX<\/strong><\/a>: Quantification of mutant-allele expression in cancer from RNA sequencing data<\/li>\n<li><a href=\"https:\/\/github.com\/eudoraleer\/scasa\"><strong>Scasa<\/strong><\/a>: A method for quantifying isoform expression from single-cell RNA-seq data from tag-based sequencing methods such as 10x Genomics<\/li>\n<li><a href=\"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/circall\/\"><strong>Circall<\/strong><\/a>: A fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data<\/li>\n<li><a href=\"https:\/\/www.meb.ki.se\/shiny\/truvu\/CircNetVis\/\"><strong>CircNetVis<\/strong><\/a>: A tool to analyze circular RNAs through circRNA:miRNA:mRNA interaction and circRNA: RNA-binding-protein (RBP) interaction.<\/li>\n<li><strong><a href=\"https:\/\/www.meb.ki.se\/sites\/biostatwiki\/xaem\/\">XAEM<\/a>:<\/strong> A method to accurately\u00a0quantify isoform expression from multiple RNA-sequencing samples.<\/li>\n<li><a href=\"https:\/\/github.com\/nghiavtr\/SCmut\"><strong>SCmut:<\/strong><\/a>\u00a0A method to detect cell-level mutation from single-cell RNA-sequencing.<\/li>\n<li><strong><a href=\"https:\/\/github.com\/nghiavtr\/FuSeq\/\">FuSeq<\/a><\/strong>: A fast method to discover fusion genes from paired-end RNA-seq data.<\/li>\n<li><strong><a href=\"https:\/\/github.com\/nghiavtr\/BPSC\">BPSC<\/a><\/strong>: An R package for model fitting and differential expression analyses of single-cell RNA-sequencing data.<\/li>\n<li><strong><a href=\"https:\/\/github.com\/nghiavtr\/ISOP\">ISOP<\/a><\/strong>: An R package for analysing isoform-level expression patterns in single-cell RNA-sequencing data.<\/li>\n<li><strong><a href=\"https:\/\/nghiavtr.shinyapps.io\/BRCAsubtypes\/\">BRCAsubtypes<\/a><\/strong>: An interactive webpage to discover subtype-specific isoforms in breast cancer data.<\/li>\n<li><a href=\"https:\/\/nghiavtr.shinyapps.io\/AMLSubtypeSpecificDiscovery\/\"><strong>AMLSubtypeSpecificDiscovery<\/strong><\/a>: An R-shiny tool for discovery of subtype-specific genes in Acute Myeloid Leukemia.<\/li>\n<li><strong><a href=\"https:\/\/github.com\/nghiavtr\/speaq\">speaq<\/a><\/strong>: An R package including a suite of informatics tools for spectral alignment and quantitative analysis of NMR metabolomic profile data.<\/li>\n<li><strong><a href=\"https:\/\/github.com\/Beirnaert\/speaq\">speaq 2.0<\/a>:<\/strong>\u00a0 A complete workflow for high-throughput 1D NMR spectra processing and quantification<\/li>\n<\/ul>\n<p>Others:<\/p>\n<ul>\n<li><strong><a href=\"https:\/\/github.com\/nghiavtr\/mascotParser\">mascotParser<\/a><\/strong>:\u00a0An R package for\u00a0parsing for Mascot search results (PMF and MSMS)<\/li>\n<\/ul>\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>I have developed (co-developed) the following bioinformatics tools: SR2P: Predicting spatial protein abundance from gene expression in spatial transcriptomics data NMF-PDR: Permutation-based Non-negative Matrix Factorization approach for drug repurposing DECLUST: A cluster-based cell-type deconvolution of spatial transcriptomic data MUSEC: Mutant-allele Isoform Explorer for cancers MegaFun: Functional quantification of microbiome from metagenomics DIPx:\u00a0Pathway activation model for [&hellip;]<\/p>\n","protected":false},"author":20,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-26","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.meb.ki.se\/sites\/truvu\/wp-json\/wp\/v2\/pages\/26","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.meb.ki.se\/sites\/truvu\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.meb.ki.se\/sites\/truvu\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.meb.ki.se\/sites\/truvu\/wp-json\/wp\/v2\/users\/20"}],"replies":[{"embeddable":true,"href":"https:\/\/www.meb.ki.se\/sites\/truvu\/wp-json\/wp\/v2\/comments?post=26"}],"version-history":[{"count":31,"href":"https:\/\/www.meb.ki.se\/sites\/truvu\/wp-json\/wp\/v2\/pages\/26\/revisions"}],"predecessor-version":[{"id":136,"href":"https:\/\/www.meb.ki.se\/sites\/truvu\/wp-json\/wp\/v2\/pages\/26\/revisions\/136"}],"wp:attachment":[{"href":"https:\/\/www.meb.ki.se\/sites\/truvu\/wp-json\/wp\/v2\/media?parent=26"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}