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• 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
• 16:19, 5 March 2024 WikiSysop talk contribs uploaded File:Document-save.png
• 16:18, 5 March 2024 WikiSysop talk contribs created page File:GOrilla webinterface1+boxes.png
• 16:18, 5 March 2024 WikiSysop talk contribs uploaded File:GOrilla webinterface1+boxes.png
• 16:17, 5 March 2024 WikiSysop talk contribs created page File:Cluster1 biological process.png
• 16:17, 5 March 2024 WikiSysop talk contribs uploaded File:Cluster1 biological process.png
• 16:16, 5 March 2024 WikiSysop talk contribs created page ExGeneOntology Yeast1.5 (Created page with "= Gene Ontology - yeast cell cycle examples = thumb|right|250px|'''Cellular component''' example: the GO term '''mitochondrion''' '''Exercise written by:''' [http://www.dtu.dk/service/telefonbog/person?id=18103&cpid=214039&tab=2&qt=dtupublicationquery Rasmus Wernersson] '''Purpose of this exercise:''' * Understand how Gene Ontology terms are defined and organized: ** The relationship between GO terms (IS A, PART OF, etc) ** The three...")
• 16:15, 5 March 2024 WikiSysop talk contribs created page ExGeneOntology Yeast R answers (Created page with "= Answers to the gene ontology exercise = Answers by Aron Eklund, created 25 November 2014.Updated by Rasmus Wernersson, October 2020. Here is a link to the exercise. leftPlease remember that the web servers and their underlying data could be updated any time, so it is possible that your results may not exactly match the results listed here. == Report question #1 == Q: ''How many ancestor terms are def...")
• 16:13, 5 March 2024 WikiSysop talk contribs created page File:Cogs brain.png
• 16:13, 5 March 2024 WikiSysop talk contribs uploaded File:Cogs brain.png
• 16:12, 5 March 2024 WikiSysop talk contribs created page File:Cluster1 subnetwork.png
• 16:12, 5 March 2024 WikiSysop talk contribs uploaded File:Cluster1 subnetwork.png
• 16:11, 5 March 2024 WikiSysop talk contribs created page File:QuickGO negative regulation example.png
• 16:11, 5 March 2024 WikiSysop talk contribs uploaded File:QuickGO negative regulation example.png
• 16:11, 5 March 2024 WikiSysop talk contribs created page File:Animal cell structure en.png
• 16:11, 5 March 2024 WikiSysop talk contribs uploaded File:Animal cell structure en.png
• 16:10, 5 March 2024 WikiSysop talk contribs created page File:QuickGO CellDivision cropped.png
• 16:10, 5 March 2024 WikiSysop talk contribs uploaded File:QuickGO CellDivision cropped.png
• 16:09, 5 March 2024 WikiSysop talk contribs created page File:QuickGO Mitochondrion.png
• 16:09, 5 March 2024 WikiSysop talk contribs uploaded File:QuickGO Mitochondrion.png
• 15:48, 5 March 2024 WikiSysop talk contribs created page ExGeneOntology Yeast R (Created page with "= Gene Ontology - yeast cell cycle examples = thumb|right|250px|'''Cellular component''' example: the GO term '''mitochondrion''' '''Exercise written by:''' [http://www.dtu.dk/service/telefonbog/person?id=18103&cpid=214039&tab=2&qt=dtupublicationquery Rasmus Wernersson] '''Purpose of this exercise:''' * Understand how Gene Ontology terms are defined and organized: ** The relationship between GO terms (IS A, PART OF, etc) ** The three...")
• 15:27, 5 March 2024 WikiSysop talk contribs created page ExYeastSysBio R answers (Created page with "= Answers to the first yeast systems biology exercise = '''Answers by:''' Lars Rønn Olsen and Rasmus Wernersson == Report questions #1 == <pre style="overflow:auto;"> library(igraph) library(ggraph) load("/home/projects/22140/exercise4.Rdata") g <- graph_from_data_frame(interactions, directed = FALSE, vertices = node_attributes) ggraph(g) + geom_edge_link(aes(color = score)) + scale_edge_color_continuous(limits = c(0,1), low = "red", high = "black") + geom_n...")
• 15:17, 5 March 2024 WikiSysop talk contribs created page File:Yeast network navigation guide CS 3.5.1.png
• 15:17, 5 March 2024 WikiSysop talk contribs uploaded File:Yeast network navigation guide CS 3.5.1.png
• 15:16, 5 March 2024 WikiSysop talk contribs created page File:YeastProteinInteractionNetwork.jpg
• 15:16, 5 March 2024 WikiSysop talk contribs uploaded File:YeastProteinInteractionNetwork.jpg
• 15:15, 5 March 2024 WikiSysop talk contribs created page File:Chromarms.gif
• 15:15, 5 March 2024 WikiSysop talk contribs uploaded File:Chromarms.gif
• 15:14, 5 March 2024 WikiSysop talk contribs created page ExYeastSysBio R (Created page with "= Exercise: Yeast Cell Cycle 1 - introduction = Exercise written by: Rasmus Wernersson and Lars Rønn Olsen = Data and databases = == Yeast genes and the Saccharomyces Genome Database == We have previously been working with UniProt based data for the exercises in week 1. UniProt is generally speaking one of the most reliable and well annotated databases out there. However, for Yeast there exists an even more dedicated database that has a 100% focus on Yeast: * The ''...")
• 15:12, 5 March 2024 WikiSysop talk contribs created page ExTopology1 igraph solutions (Created page with "= Exercise: Network topology and statistics = '''Exercise written by: Lars Rønn Olsen''' Notes on today's exercise: today we will get a bit more advanced in our use of igraph. If you get stuck, remember that ''Google and chatGPT are your friends.'' == Part I. Getting started == <pre style="overflow:auto;"> load("/home/projects/22140/exercise3.Rdata") </pre> '''TASK: Create an igraph object with node attributes''' <pre style="overflow:auto;"> g <- graph_from_data_f...")
• 15:12, 5 March 2024 WikiSysop talk contribs created page ExTopology1 igraph (Created page with "= Exercise: Network topology and statistics = '''Exercise written by: Lars Rønn Olsen''' Notes on today's exercise: today we will get a bit more advanced in our use of igraph. If you get stuck, remember that ''Google and chatGPT are your friends.'' == Part I. Getting started == In this exercise we will use a subset of the human interaction dataset by Rual et al. (Nature.2005 Oct 20;437(7062):1173-8). The data consists of an interaction data frame (without edge annot...")
• 15:06, 5 March 2024 WikiSysop talk contribs created page Ex handouts igraph solution (Created page with "= Part 1 - network from AP/MS data = Interaction data from exercise 5 and edge scores from exercise 6 <pre style="overflow:auto;"> library(igraph) library(ggraph) ex5_interactions <- data.frame(from = c("A", "B", "B", "B", "B", "B", "D", "D", "E", "F", "F"), to = c("B", "C", "D", "E", "F", "H", "F", "G", "H", "G", "H"), score = c(-0.155, -0.234, -0.222, -0.183, -0.183, -0.183, -0.301, -0.194, -0.301, -0.301, -0.301)) g <- graph_from_data_frame(ex5_interactions, d...")
• 15:06, 5 March 2024 WikiSysop talk contribs created page Ex handouts igraph (Created page with "= PPI Data visualization: extension to the hand-out exercise = Exercise written by Lars Rønn Olsen and Rasmus Wernersson This is a short igraph visualization exercise based on the networks and scores derived in the hand-out exercises. == Part 1 - network from AP/MS data == 30px|left'''Part 1''' * Create a data frame based on the network derived from '''exercise 5''' * Create an edge annotation vector based on the scores calcul...")
• 15:05, 5 March 2024 WikiSysop talk contribs created page File:Exercise help sheet.pdf
• 15:05, 5 March 2024 WikiSysop talk contribs uploaded File:Exercise help sheet.pdf
• 15:03, 5 March 2024 WikiSysop talk contribs created page File:W02 exercises v7 corrected.pdf
• 15:03, 5 March 2024 WikiSysop talk contribs uploaded File:W02 exercises v7 corrected.pdf
• 15:01, 5 March 2024 WikiSysop talk contribs created page File:Extended pold w attributes.png
• 15:01, 5 March 2024 WikiSysop talk contribs uploaded File:Extended pold w attributes.png
• 15:00, 5 March 2024 WikiSysop talk contribs created page File:POLD excel after.png
• 15:00, 5 March 2024 WikiSysop talk contribs uploaded File:POLD excel after.png
• 14:59, 5 March 2024 WikiSysop talk contribs created page File:Pold w node attributes.png
• 14:59, 5 March 2024 WikiSysop talk contribs uploaded File:Pold w node attributes.png
• 14:58, 5 March 2024 WikiSysop talk contribs created page IgraphIntro Answers v1 (Created page with "= Aswers: " Cytoscape and network intro exercise" = '''Answers by:''' Lars Rønn Olsen and Rasmus Wernersson = Item #1: Loading network as an igraph object = <pre style="overflow:auto;"> library(igraph) df <- data.frame(from = c("alpha", "alpha", "beta"), to = c("alpha", "beta", "beta")) g <- graph_from_data_frame(df, directed = FALSE) </pre> = Item #2: Node attributes and visualization = <pre style="overflow:auto;"> poldelta_graph <- data.frame(from = c("DPOD1_HUMAN"...")