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Combined display of all available logs of 22140. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

10:30, 14 November 2024 User account Krivi talk contribs was created by WikiSysop talk contribs
10:28, 14 November 2024 User account Dimkan talk contribs was created by WikiSysop talk contribs
08:34, 27 August 2024 User account Lronn talk contribs was created by WikiSysop talk contribs
10:27, 18 March 2024 WikiSysop talk contribs created page Autumn2021 (Created page with "= Course 22140 (previously 36040) - plan for autumn 2021 =  '''Teachers:''' * [https://www.biosurf.org Lars Rønn Olsen] (course organizer) - '''contact:''' [mailto:lronn@dtu.dk lronn@dtu.dk] * Kristoffer Vitting-Seerup (course organizer) - '''contact:''' [mailto:krivi@dtu.dk krivi@dtu.dk] * [http://www.cbs.dtu.dk/~raz/ Rasmus Wernersson] (lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk] * Giorgia Moranzoni (teaching assistant...")
17:12, 5 March 2024 WikiSysop talk contribs created page File:Cytoscape icon.png
17:12, 5 March 2024 WikiSysop talk contribs uploaded File:Cytoscape icon.png
17:11, 5 March 2024 WikiSysop talk contribs created page Autumn2022 (Created page with "= Course 22140 (previously 36040) - plan for autumn 2022 =  '''Teachers:''' * Kristoffer Vitting-Seerup (course organizer) - '''contact:''' [mailto:krivi@dtu.dk krivi@dtu.dk] * [http://www.cbs.dtu.dk/~raz/ Rasmus Wernersson] (external lecturer) - '''contact:''' [mailto:rawe@dtu.dk rawe@dtu.dk] * Giorgia Moranzoni (teaching assistant) - '''contact:''' [mailto:gimo@dtu.dk gimo@dtu.dk] * Lars Rønn Olsen (course organizer) is on parental lea...")
17:09, 5 March 2024 WikiSysop talk contribs created page File:Community2.png
17:09, 5 March 2024 WikiSysop talk contribs uploaded File:Community2.png
17:09, 5 March 2024 WikiSysop talk contribs created page DiscoNet2 answers (Created page with "= Multiomics data integration exercise - Answers = '''Answers written by:''' Lars Rønn Olsen First, load the data for today's exercise: <pre> load("/home/projects/22140/exercise10.Rdata") </pre> Then, randomly pick a patient number. Let's use R to make sure it is random: <pre> sample(1:10, 1) </pre> For that patient calculate the log2 fold change of gene expression in cancer vs normal log2(cancer expression / normal expression). Consider genes with a log2 fold chan...")
17:08, 5 March 2024 WikiSysop talk contribs created page DiscoNet2 (Created page with "= Multiomics data integration exercise = '''Exercise written by:''' Lars Rønn Olsen '''Learning objectives:''' * Overall objective: learn how to extract meaningful networks from human PPI data *# Virtual pulldowns: sampling 1st order networks and filtering "sticky proteins" *# Finding tightly connected clusters in larger networks *# Using the DiscoNet package in R == Introduction == Today’s exercise requires the use of many of the methods you learned throughout this...")
17:05, 5 March 2024 WikiSysop talk contribs created page File:Community2 w9.png
17:05, 5 March 2024 WikiSysop talk contribs uploaded File:Community2 w9.png
17:04, 5 March 2024 WikiSysop talk contribs created page File:Community1.png
17:04, 5 March 2024 WikiSysop talk contribs uploaded File:Community1.png
17:04, 5 March 2024 WikiSysop talk contribs created page File:G3.png
17:04, 5 March 2024 WikiSysop talk contribs uploaded File:G3.png
17:03, 5 March 2024 WikiSysop talk contribs created page File:G2.png
17:03, 5 March 2024 WikiSysop talk contribs uploaded File:G2.png
17:03, 5 March 2024 WikiSysop talk contribs created page File:G1.png
17:03, 5 March 2024 WikiSysop talk contribs uploaded File:G1.png
17:02, 5 March 2024 WikiSysop talk contribs created page DiscoNet answers (Created page with "= Human diseases / virtual pulldown exercise = '''Exercise written by:''' Lars Rønn Olsen, Giorgia Moranzoni, and Rasmus Wernersson 30px|left '''TASK/REPORT QUESTION #1:''' # Load the packages <pre> library(DiscoNet) library(msigdbr) library(fgsea) The PPI database we will use is InWeb: db <- translate_database("inweb") </pre> # Run DiscoNet with this list of proteins with the following parameters: <pre> network_ex2 <- virtu...")
17:00, 5 March 2024 WikiSysop talk contribs created page File:Heart+networks.png
17:00, 5 March 2024 WikiSysop talk contribs uploaded File:Heart+networks.png
16:56, 5 March 2024 WikiSysop talk contribs created page DiscoNet (Created page with "= Human diseases / virtual pulldown exercise = '''Exercise written by:''' Lars Rønn Olsen, Giorgia Moranzoni, and Rasmus Wernersson '''Learning objectives:''' * Overall objective: learn how to extract meaningful networks from human PPI data *# Virtual pulldowns: sampling 1st order networks and filtering "sticky proteins" *# Finding tightly connected clusters in larger networks *# Using the DiscoNet package in R == Introduction == Image:Heart+networks.png|600px|right...")
16:54, 5 March 2024 WikiSysop talk contribs created page File:XKCD significant.png
16:54, 5 March 2024 WikiSysop talk contribs uploaded File:XKCD significant.png
16:51, 5 March 2024 WikiSysop talk contribs created page ExYeastCellCycleTranscriptomics2 R answers (Created page with "===Question 1=== <pre> library(igraph) library(ggraph) load("home/projects/22140/exercise4.Rdata") load("home/projects/22140/exercise6.Rdata") expr$log2fc <- log2(expr$GSM287992/expr$GSM287991) node_attributes_updated <- merge(x = node_attributes, y = expr[!duplicated(expr$SysName),c(1,6)], by.x = "ID", by.y = "SysName", all.x = TRUE) g <- graph_from_data_frame(interactions, directed = FALSE, vertices = node_attributes_updated) ggraph(g) + geom_edge_link() + g...")
16:49, 5 March 2024 WikiSysop talk contribs created page File:YBL002W.cdc15.png
16:49, 5 March 2024 WikiSysop talk contribs uploaded File:YBL002W.cdc15.png
16:49, 5 March 2024 WikiSysop talk contribs created page File:YBL002W.30.png
16:49, 5 March 2024 WikiSysop talk contribs uploaded File:YBL002W.30.png
16:48, 5 March 2024 WikiSysop talk contribs created page File:HTB2-peaktime.png
16:48, 5 March 2024 WikiSysop talk contribs uploaded File:HTB2-peaktime.png
16:46, 5 March 2024 WikiSysop talk contribs created page File:YKL185W.30.png
16:46, 5 March 2024 WikiSysop talk contribs uploaded File:YKL185W.30.png
16:45, 5 March 2024 WikiSysop talk contribs created page ExYeastCellCycleTranscriptomics2 R (Created page with "= Yeast cell cycle / transcriptomics exercise #2 = '''Exercise written by:''' Rasmus Wernersson and Lars Rønn Olsen = PART 1: Network analysis of the Alpha Factor Arrest data = left IMPORTANT: We continue working with the data set from week 4. == Network analysis == The final part of the analysis of the alpha-factor arrest data set we started in the previous exercise, is to map it onto the Yeast protein-protein interaction netwo...")
16:30, 5 March 2024 WikiSysop talk contribs created page ExYeastCellCycle answers (Created page with "===Question 1=== Q:How much RNA ("total RNA") was used in the experiment? A: 50 ug of total RNA (found on the Protocols page). Q: Which type/brand of array was used? A: Affymetrix GeneChip Yeast Genome 2.0 Array (found on the main page). Q: How many individual arrays were used in the study? A: 2 arrays (found both on the main page and the samples page) Q: IMPORTANT: note down which arrays were used for CONTROL (asynchronous; "mock treated") and which were use for CAS...")
16:28, 5 March 2024 WikiSysop talk contribs created page File:Log2 graph.png
16:28, 5 March 2024 WikiSysop talk contribs uploaded File:Log2 graph.png
16:27, 5 March 2024 WikiSysop talk contribs created page File:Checkmark from openclipart.png
16:27, 5 March 2024 WikiSysop talk contribs uploaded File:Checkmark from openclipart.png
16:27, 5 March 2024 WikiSysop talk contribs created page ExYeastCellCycleTranscriptomics R (Created page with "= Yeast cell cycle / transcriptomics exercise #1 = '''Exercise written by:''' Rasmus Wernersson and Lars Rønn Olsen '''Learning objectives:''' * Introduction to practical work on array CASE/CONTROL studies. * Introduction to ArrayExpress as a way to download DNA microarray experimental data. * Introduction to basic expression data transformation: ** Calculation of Log2 expression values ** Basic evaluation of the comparability of two arrays. ** Calculation of FOLD CHA...")
16:23, 5 March 2024 WikiSysop talk contribs created page File:Graphpad pvalue 02.png
16:23, 5 March 2024 WikiSysop talk contribs uploaded File:Graphpad pvalue 02.png
16:22, 5 March 2024 WikiSysop talk contribs created page File:Graphpad pvalue 01.png
16:22, 5 March 2024 WikiSysop talk contribs uploaded File:Graphpad pvalue 01.png
16:22, 5 March 2024 WikiSysop talk contribs created page File:DNA pol act tree.png
16:22, 5 March 2024 WikiSysop talk contribs uploaded File:DNA pol act tree.png
16:19, 5 March 2024 WikiSysop talk contribs created page File:Document-save.png

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