{"id":11,"date":"2021-04-14T14:01:45","date_gmt":"2021-04-14T14:01:45","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/training\/materials\/template\/programme\/"},"modified":"2025-02-24T11:16:32","modified_gmt":"2025-02-24T11:16:32","slug":"programme-2","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-handbook-2025\/programme-2\/","title":{"rendered":"Programme"},"content":{"rendered":"\n

All sessions will take place using Zoom, please join using the \u2018Join Zoom\u2019 button. Password: SingCell<\/strong><\/p>\n\n\n\n

If you have any problems using Zoom, please first check the Zoom help sheet<\/a>. <\/p>\n\n\n\n

If you have watched the pre-recordings before the course, then the times marked in the programme for the pre-recorded sessions are for you to use as you wish. Please make sure you add any questions from the pre-recording to the course Q&A document<\/a>.<\/p>\n\n\n\n

All programme times are in GMT, to make sure you join sessions at the correct time, you can check the\u00a0current GMT time here<\/a>.<\/p>\n\n\n\n

Data and containers from the course can be found in the EBI FTP<\/a>, available for all to download.<\/p>\n\n\n\n

\n
Join Zoom<\/a><\/div>\n<\/div>\n\n\n\n

<\/p>\n\n\n\n

Time<\/strong><\/td>Topic<\/strong><\/td>Trainer<\/strong><\/td><\/tr>
Day one \u2013 Monday 17 February – Planning the experiment<\/a><\/strong><\/td><\/tr>
09:00 \u2014 09:45<\/td>Introduction to EMBL-EBI and icebreaker<\/td>Piv Gopalasingam<\/td><\/tr>
09:45 \u2014 10:00<\/strong><\/td>Break<\/strong><\/td><\/td><\/tr>
10:00 \u2014 10:45<\/td>Introduction to Single Cell Technologies<\/td>Silvie Fexova<\/td><\/tr>
10:45 \u2014 12:15<\/td>Wet-lab overview <\/td>Wendi Bacon<\/td><\/tr>
12:15 \u2014 13:15<\/strong><\/td>Lunch break<\/strong><\/td><\/td><\/tr>
13:15  \u2014 14:30<\/td>Dry-lab overview<\/td>Wendi Bacon<\/td><\/tr>
14:30 \u2014 15:00<\/strong><\/td>Break<\/strong><\/td><\/td><\/tr>
15:00 \u2014 16:30<\/td>Experimental design and Q&A<\/td>Tallulah Andrews<\/td><\/tr>
Day two \u2013 Tuesday 18 February – Processing data<\/a><\/strong><\/td><\/tr>
08:00 \u2014 09:00<\/td>Designing your analysis (pre-recorded)<\/td>Tallulah Andrews<\/td><\/tr>
09:00 \u2014 09:40<\/td>Getting set up: data set, workflow and environment setup<\/td>Anna Vathrakokoili Pournara<\/td><\/tr>
09:40 – 10:00 <\/strong><\/td>Break  <\/strong><\/td> <\/td><\/tr>
10:00 \u2014 11:00 <\/td>Raw reads to expression matrix  \u2014 Talk and Q&A<\/td>Jiawei Wang and Jinzheng Ren<\/td><\/tr>
11:00 \u2014 12:30 <\/td>QC, Pre-processing, & Normalisation (pre-recorded talk and practical demo)<\/td> Yuyao Song, Hugo Tavares and Iris Yu<\/td><\/tr>
12:30 \u2014 13:30  <\/strong><\/td>Lunch break  <\/strong><\/td> <\/td><\/tr>
13:30 \u2014 14:20 <\/td>Feature selection and dimensionality reduction \u2014 Talk and Q&A<\/td>Anna Vathrakokoili Pournara<\/td><\/tr>
14:20 \u201415:00<\/td>Batch correction and data set integration \u2014 Talk and Q&A<\/td>Yuyao Song<\/td><\/tr>
15:00 \u2014 15:30  <\/strong><\/td>Break<\/strong><\/td><\/td><\/tr>
15:30 \u2014 16:30<\/strong><\/td>Posters and Networking  <\/strong><\/td> <\/td><\/tr>
Day three \u2013 Wednesday 19 February – Analysing data<\/a><\/strong><\/td><\/tr>
09:00 \u2014 10:00<\/td>Feature Selection, Dimensionality Reduction, and Data Integration \u2014 Practicals<\/td>Yuyao Song<\/td><\/tr>
10:00 \u2014 10:20<\/strong><\/td>Break<\/strong><\/td><\/td><\/tr>
10:20 \u2014 11:30<\/td>Clustering and Cluster Marker Genes \u2014 Practicals<\/td>Anna Vathrakokoili Pournara<\/td><\/tr>
11:30 \u2014 12:30<\/td>Differential Expression and Abundance Analysis \u2014 Talk and Q&A<\/td>Andrian Yang<\/td><\/tr>
12:30 \u2014 13:30  <\/strong><\/td>Lunch break  <\/strong><\/td><\/td><\/tr>
13:30 \u2014 14:30<\/td>Differential Expression \u2014 Practical<\/td>Andrian Yang<\/td><\/tr>
14:30 \u2014 15:30<\/td>Abundance Analysis  \u2014 Practical<\/td>Andrian Yang<\/td><\/tr>
15:30\u2014 16:30<\/strong><\/td>Poster and Networking<\/strong><\/td><\/td><\/tr>
Day four \u2013 Thursday 20 February – Applying the pipeline<\/a><\/strong><\/td><\/tr>
09:00 \u2014 09:40<\/td>Spatial transcriptomics \u2014 Talk and Q&A<\/td>Nadav Yayon<\/td><\/tr>
09:40 \u2014 10:00<\/strong><\/td>Break<\/strong><\/td><\/td><\/tr>
10:00 \u2014 12:00<\/td>Spatial transcriptiomics \u2014 Practical<\/td>Nadav Yayon<\/td><\/tr>
12:00 \u2014 13:00 <\/strong><\/td>Lunch break<\/strong><\/td> <\/strong><\/td><\/tr>
13:00 \u2014 14:00<\/td>Single cell Expression Atlas and single cell data submission<\/td>Liora Vilmovsky and Silvie Fexova<\/td><\/tr>
14:00 \u2014 15:00<\/td>Project work<\/td>Project mentors<\/td><\/tr>
15:00 \u2014 15:30<\/strong><\/td>Break <\/strong><\/td> <\/strong><\/td><\/tr>
15:30 \u2014 16:00<\/td>Project work<\/td>Project mentors<\/td><\/tr>
Day five \u2013 Friday 21 February – Putting it into practice<\/a><\/strong><\/td><\/tr>
09:00 \u2014 10:00  <\/td>Project work<\/td>Project mentors<\/td><\/tr>
10:00 \u2014 10:20  <\/strong><\/td>Break <\/strong><\/td> <\/td><\/tr>
10:20 \u2014 12:00  <\/td>Project work <\/td>Project mentors<\/td><\/tr>
12:00 \u2014 13:00  <\/strong><\/td>Lunch break <\/strong><\/td> <\/strong><\/td><\/tr>
13:00 \u2014 14:00<\/td>Project work wrap-up<\/td>Project mentors<\/td><\/tr>
14:00 \u2014 15:00<\/td>Final Q&A with project mentors<\/td><\/td><\/tr>
15:00 \u2014 15:30<\/td>Course wrap-up and survey<\/td>Piv Gopalasingam<\/td><\/tr><\/tbody><\/table><\/figure>\n","protected":false},"excerpt":{"rendered":"

All sessions will take place using Zoom, please join using the \u2018Join Zoom\u2019 button. Password: SingCell If you have any problems using Zoom, please first check the Zoom help sheet. If you have watched the pre-recordings before the course, then the times marked in the programme for the pre-recorded sessions are for you to use as…<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-11","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-handbook-2025\/wp-json\/wp\/v2\/pages\/11","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-handbook-2025\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-handbook-2025\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-handbook-2025\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-handbook-2025\/wp-json\/wp\/v2\/comments?post=11"}],"version-history":[{"count":95,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-handbook-2025\/wp-json\/wp\/v2\/pages\/11\/revisions"}],"predecessor-version":[{"id":3431,"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-handbook-2025\/wp-json\/wp\/v2\/pages\/11\/revisions\/3431"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/training\/materials\/single-cell-rna-seq-analysis-using-python-handbook-2025\/wp-json\/wp\/v2\/media?parent=11"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}