User: biohacker_tobe

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Posts by biohacker_tobe

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Comment: C: Creating a Contingency Table (Gene Absence Presence)
... Hi I wanted to ask something about this heatmap you mentioned here, you mentioned I could do it on a matrix like this: BGC1 BGC2 Distance ----------------------------------------------- BGC31 BGC34 0.6 BGC34 BGC45 0.7 BGC34 BGC53 0.2 BGC53 ...
written 3 days ago by biohacker_tobe20
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Comment: C: Co-Occurrence Network Graph & Statistics
... As you have mentioned my binary matrix is non-square matrix, is it possible to change this to square matrix? The first method provided gave me an error when trying to run: Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : At structure_generators.c:274 : Non- ...
written 3 days ago by biohacker_tobe20
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Co-Occurrence Network Graph & Statistics
... I am trying to make a co-occurrence network graph for my presence/absence data of genes per genomes but am unsure how to go about with it. I'm hoping to end up with something like the first image below, Where each gene is linked to another gene , considering if they are both present in the same gen ...
R networks dataframe written 4 days ago by biohacker_tobe20 • updated 3 days ago by Jean-Karim Heriche21k
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Comment: C: Co-Ocurrence between Bacteria Gene Clusters
... That is true, I just wanted a different reference but I will delete this post to avoid any mislead. Thanks and sorry for the inconvenience! ...
written 10 days ago by biohacker_tobe20
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Comment: C: Creating a Contingency Table (Gene Absence Presence)
... I will check this out. It's just in my case there are no particular GC pairs of interest, I just want to look at the overall behavior for this? Thanks again stuart for taking time to answer my questions :) ...
written 10 days ago by biohacker_tobe20
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Comment: C: Creating a Contingency Table (Gene Absence Presence)
... Sorry I didn't mean to have a lack of clarification in my questions in this regards. But it is as you have mentioned: 1) Unfortunately I am not able to make my matrix symmetric, for which I am not able to complete the tree with the dendrogram. Thank you though for the assistance on this. 2) In thi ...
written 11 days ago by biohacker_tobe20
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Comment: C: Gene Cluster Phylogenetic Tree
... is it possible to delete the comments? ...
written 12 days ago by biohacker_tobe20
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Comment: C: Creating a Contingency Table (Gene Absence Presence)
... @Stuart I have no way to thank you for your help on all of this, this is a big help for myself and to fine tune my project. I have been able to previously run an algorithm that measures the phylogenetic relationship between gene clusters, so the distances in this case are definitely based on how clo ...
written 12 days ago by biohacker_tobe20
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Comment: C: Creating a Contingency Table (Gene Absence Presence)
... @stuart When I was talking about constructing a tree, it was based on these distances as I mentioned above. I was just curious that if I could actually do clulstering from this based on distances between BGC types, in this case I'm not interested in the strains themselves: BGC1 BGC2 Di ...
written 12 days ago by biohacker_tobe20
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Comment: C: Creating a Contingency Table (Gene Absence Presence)
... Thanks for your input on this, I will try the revision of a binary matrix based on packages mentioned. I just want a binary matrix more or less so I can eventually plot a heatmap and conduct statistical analysis, even something simple such as chi squared to measure the proper correlation. Thanks a ...
written 14 days ago by biohacker_tobe20

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