{"id":93,"date":"2021-03-18T21:10:05","date_gmt":"2021-03-18T21:10:05","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/turrolab\/?page_id=93"},"modified":"2023-03-08T22:04:21","modified_gmt":"2023-03-08T22:04:21","slug":"software","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/turrolab\/software\/","title":{"rendered":"Software"},"content":{"rendered":"<ul>\n<li><a href=\"https:\/\/github.com\/turrogroup\/rsvr\">Rareservoir<\/a>: a database schema and associated tools for working with rare variant and rare disease data. <a href=\"https:\/\/doi.org\/10.1038\/s41591-023-02211-z\">Greene et al (2023).<\/a><\/li>\n<li><a href=\"https:\/\/mitophen.org\">MitoPhen<\/a>: a database of mitochondrial disease variants and patients. <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkab726\">Ratnaike, Greene et al (2021).<\/a><\/li>\n<li><a href=\"https:\/\/cran.r-project.org\/web\/packages\/BeviMed\/\">BeviMed<\/a>: statistical method for performing Bayesian evaluation of variant involvement in Mendelian disease. <a href=\"http:\/\/dx.doi.org\/10.1016\/j.ajhg.2017.05.015\">Greene et al (2017).<\/a><\/li>\n<li><a href=\"https:\/\/cran.r-project.org\/web\/packages\/ontologyIndex\/index.html\">OntologyX<\/a>: R packages for working with ontological data. <a href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btw763\">Greene et al (2017).<\/a><\/li>\n<li><a href=\"https:\/\/cran.r-project.org\/web\/packages\/SimReg\/index.html\">SimReg<\/a>: Bayesian phenotype similarity regression for identifying associations between Human Phenotype Ontology (HPO)-coded patient phenotypes and genotypes at rare variant sites. <a href=\"http:\/\/dx.doi.org\/10.1016\/j.ajhg.2016.01.008\">Greene et al (2016)<\/a><\/li>\n<li><a href=\"https:\/\/github.com\/eturro\/mmseq\">MMDIFF<\/a>: software for flexible analysis of RNA-seq data using Bayesian mixed effects models. <a href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btt624\">Turro et al (2014)<\/a><\/li>\n<li><a href=\"https:\/\/github.com\/eturro\/mmseq\">MMSEQ<\/a>: widely used software for Bayesian haplotype, isoform and gene specific expression estimation using multi-mapping RNA-seq reads. <a href=\"http:\/\/dx.doi.org\/10.1186\/gb-2011-12-2-r13\">Turro et al (2011).<\/a><\/li>\n<li><a href=\"http:\/\/bgx.org.uk\/software\/mmbgx.html\">MMBGX<\/a>: a Bayesian method for estimating expression at the isoform and gene level and detecting differential splicing using whole-transcript Affymetrix arrays. <a href=\"http:\/\/dx.doi.org\/10.1093\/nar\/gkp853\">Turro et al (2010)<\/a>.<\/li>\n<li><a href=\"http:\/\/bioconductor.org\/packages\/release\/bioc\/html\/bgx.html\">BGX<\/a>: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips. <a href=\"http:\/\/dx.doi.org\/10.1186\/1471-2105-8-439\">Turro et al (2007)<\/a>.<\/li>\n<\/ul>\n<p>Find us on <a href=\"https:\/\/github.com\/turrogroup\">GitHub<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Rareservoir: a database schema and associated tools for working with rare variant and rare disease data. Greene et al (2023). MitoPhen: a database of mitochondrial disease variants and patients. Ratnaike, Greene et al (2021). BeviMed: statistical method for performing Bayesian evaluation of variant involvement in Mendelian disease. Greene et al (2017). OntologyX: R packages for [&hellip;]<\/p>\n","protected":false},"author":459,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-93","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/turrolab\/wp-json\/wp\/v2\/pages\/93","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/turrolab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/turrolab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/turrolab\/wp-json\/wp\/v2\/users\/459"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/turrolab\/wp-json\/wp\/v2\/comments?post=93"}],"version-history":[{"count":12,"href":"https:\/\/labs.icahn.mssm.edu\/turrolab\/wp-json\/wp\/v2\/pages\/93\/revisions"}],"predecessor-version":[{"id":175,"href":"https:\/\/labs.icahn.mssm.edu\/turrolab\/wp-json\/wp\/v2\/pages\/93\/revisions\/175"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/turrolab\/wp-json\/wp\/v2\/media?parent=93"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}