{"id":198,"date":"2021-07-27T13:54:20","date_gmt":"2021-07-27T13:54:20","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-materials\/pre-course-homework\/pre-precessing-and-dimensionality-reduction\/"},"modified":"2023-11-02T14:13:39","modified_gmt":"2023-11-02T14:13:39","slug":"pre-processing-and-dimensionality-reduction","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/analysing-data\/pre-processing-and-dimensionality-reduction\/","title":{"rendered":"Pre-processing and dimensionality reduction"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\"><strong>Trainer:<\/strong> <a href=\"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/trainers-biographies\/\">Alsu Missarova and Ana-Maria Cujba<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Overview:<\/strong> In this session, you will work on the pre-processing and dimensionality reduction of a given dataset.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Learning outcomes:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Load data and create a Seurat object<\/li><li>Check the quality of the cells and remove low-quality data<\/li><li>Normalise and scale the data<\/li><li>Perform gene signature scoring<\/li><li>Batch correction<\/li><li>Remove ambient RNA contamination<\/li><li>Remove doublets<\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Materials:<\/strong><\/p>\n\n\n\n<iframe loading=\"lazy\" src=\"https:\/\/embl-ebi.cloud.panopto.eu\/Panopto\/Pages\/Embed.aspx?id=b4048281-8da6-4ada-b058-af2300854853&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<ul class=\"wp-block-list\"><li><a href=\"https:\/\/drive.google.com\/file\/d\/175lYDYCgty7NDru3W-JawSCKf3F0dJ2E\/view?usp=drive_link\">Presentation slides<\/a><\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Practical:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/drive.google.com\/file\/d\/1AEgQxzUpz_eHrFilcUU5mQfpfWolt3q6\/view?usp=sharing\" target=\"_blank\" rel=\"noreferrer noopener\">Tutorial<\/a><\/li><li><a href=\"https:\/\/drive.google.com\/file\/d\/1NAfF-PDL8ygeRjcNKE1Rn3OzXSnmSlhn\/view?usp=sharing\" target=\"_blank\" rel=\"noreferrer noopener\">Answer key<\/a><\/li><\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Trainer: Alsu Missarova and Ana-Maria Cujba Overview: In this session, you will work on the pre-processing and dimensionality reduction of a given dataset. Learning outcomes: Load data and create a Seurat object Check the quality of the cells and remove low-quality data Normalise and scale the data Perform gene signature scoring Batch correction Remove ambient&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":17,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-198","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\/198","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=198"}],"version-history":[{"count":13,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages\/198\/revisions"}],"predecessor-version":[{"id":835,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-r\/wp-json\/wp\/v2\/pages\/198\/revisions\/835"}],"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=198"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}