{"id":541,"date":"2022-10-26T15:57:02","date_gmt":"2022-10-26T15:57:02","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r-temp\/analysing-data\/designing-your-analysis\/"},"modified":"2023-01-10T16:25:01","modified_gmt":"2023-01-10T16:25:01","slug":"designing-your-analysis","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/analysing-data\/designing-your-analysis\/","title":{"rendered":"Designing your analysis"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\"><strong>Trainer:<\/strong>\u00a0<a href=\"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/trainers-biographies\/\">Tallulah Andrews<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Overview:<\/strong> In the training session,  I will discuss when and where to apply different analysis tools and how inappropriate use of these tools can lead to false conclusions.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Learning outcomes:<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">By the end of the session you will be able to:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Recognise decision-making steps along the analysis pipeline and justify your decisions.<\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Materials:<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Lecture<\/p>\n\n\n\n<iframe loading=\"lazy\" src=\"https:\/\/embl-ebi.cloud.panopto.eu\/Panopto\/Pages\/Embed.aspx?id=8ddcb5e0-463e-4366-b8ac-af23008675fb&amp;autoplay=false&amp;offerviewer=true&amp;showtitle=true&amp;showbrand=true&amp;captions=false&amp;interactivity=all\" height=\"405\" width=\"720\" style=\"border: 1px solid #464646;\" allowfullscreen=\"\" allow=\"autoplay\"><\/iframe>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/docs.google.com\/presentation\/d\/1n9ceDgFh9J7eAFqPgM6M6cjWjscZCYUB\/edit?usp=sharing&amp;ouid=107001233493882804410&amp;rtpof=true&amp;sd=true\" target=\"_blank\" rel=\"noreferrer noopener\">Presentation slides<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Further reading<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Benchmarking studies:<br><a rel=\"noreferrer noopener\" href=\"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-019-1795-z\" target=\"_blank\">Automatic annotation<\/a><br><a rel=\"noreferrer noopener\" href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2217-z\" target=\"_blank\">Gene regulatory networks<\/a><br><a rel=\"noreferrer noopener\" href=\"https:\/\/f1000research.com\/articles\/7-1141\/v3\" target=\"_blank\">Clustering<\/a><br><a rel=\"noreferrer noopener\" href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2019.12.19.877522v1\" target=\"_blank\">UMAP vs tSNE<\/a><br><a rel=\"noreferrer noopener\" href=\"https:\/\/www.nature.com\/articles\/s41587-019-0071-9\" target=\"_blank\">Pseudotime<\/a><br><a rel=\"noreferrer noopener\" href=\"https:\/\/www.nature.com\/articles\/nmeth.4612\" target=\"_blank\">Differential expression<\/a><br><a rel=\"noreferrer noopener\" href=\"https:\/\/sciwheel.com\/fulltext\/doi\/10.12688\/f1000research.16613.2\" target=\"_blank\">Imputation<\/a><br><\/li><li>Reviews:<br><a rel=\"noreferrer noopener\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0098299717300493?via%3Dihub\" target=\"_blank\">Clustering<\/a><br><a rel=\"noreferrer noopener\" href=\"https:\/\/www.nature.com\/articles\/s41596-020-00409-w\" target=\"_blank\">Whole analysis<\/a><br><\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Trainer:\u00a0Tallulah Andrews Overview: In the training session, I will discuss when and where to apply different analysis tools and how inappropriate use of these tools can lead to false conclusions. Learning outcomes: By the end of the session you will be able to: Recognise decision-making steps along the analysis pipeline and justify your decisions. Materials:&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":17,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-541","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages\/541","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/comments?post=541"}],"version-history":[{"count":7,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages\/541\/revisions"}],"predecessor-version":[{"id":821,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages\/541\/revisions\/821"}],"up":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages\/17"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/media?parent=541"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}