User: tpm

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tpm10
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Posts by tpm

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compareCluster - E coli K12 EnrichKegg error
... Hello. I am using clusterProfiler R package. I am trying to make a visualize result using a dotplot graph for my data. It seems I am facing a stumbling block on the final analysis using `compareCluster`. I am working with E. coliK12 strain and I want to perform an enrichment analysis with Kegg (`enr ...
bioconductor clusterprofiler comparecluster written 6 hours ago by tpm10
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Comment: C: How to simultaneously convert gene IDs to Kegg IDs for E. coli
... I will run the code again I suppose. Thanks for the timely responses, much appreciated. ...
written 10 hours ago by tpm10
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Comment: C: How to simultaneously convert gene IDs to Kegg IDs for E. coli
... I do see this output when I run the `keytypes(org.EcK12.eg.db)` , but I cannot see the `KEGG` option. In order to perform compareCluster function on `clusterProfiler`, the IDs should be in `KEGG` format. Initially at least, I wanted to convert using one of these options. ...
written 15 hours ago by tpm10
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Comment: C: How to simultaneously convert gene IDs to Kegg IDs for E. coli
... Hi, thanks Kevin, It seems that keytypes for E coil K12 do not have keggID option. I can't seem to find the keyType for "kegg" option at least for me. From the: keytype(org.EcK12.eg.db) I want to perform enrichKEGG on compareCluste. That's why I am kindly asking if there was a way to avoid thi ...
written 17 hours ago by tpm10
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Comment: C: kegg id convertion
... did you manage to figure it out yet? Try this https://www.genome.jp/kegg/tool/conv_id.html ...
written 1 day ago by tpm10
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How to simultaneously convert gene IDs to Kegg IDs for E. coli
... Hi guys, How do I convert these gene IDs to Kegg IDs for E.coli at the same time. I tried this link but somehow I`m not successful (https://www.genome.jp/kegg/tool/conv_id.html). An example shown are these sample set of genes below: nupX psuT atpE rnlA yiiM zapE eutC ...
bioconductor kegg geneid written 1 day ago by tpm10 • updated 1 day ago by Kevin Blighe59k
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Comment: C: What codes do I use to generate gene cluster vectors with entrez gene id on clus
... Thank you very much this is helpful a lot. ...
written 2 days ago by tpm10
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compareProfiler - Assistance on how I can modify codes for different states
... My question is related to the tutorial from this link (https://yulab-smu.github.io/clusterProfiler-book/chapter11.html#formula-interface-of-comparecluster). From this code below, what needs to be modified in order to add more groups if I have “A”, “B”, “C”, “D”....when I don’t only have "A" and "B" ...
assembly bioconductor clusterprofiler R written 2 days ago by tpm10
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Comment: A: What codes do I use to generate gene cluster vectors with entrez gene id on clus
... For each set (X1 to X4) is the gene and the corresponding logFC. For example, this is an example of my dataset if I take just a few samples from it: X1 galF 0.039335412 adhE -0.407887182 ribE 0.039104767 mlaC -0.183376255 cspE 0.020263717 insC1 1.275285226 dps -0.229873 ...
written 3 days ago by tpm10
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What codes do I use to generate gene cluster vectors with entrez gene id on clusterProfiler.
... Hi guys, I am very new on R. I have 4 csv files with gene sets X1, X2, X3, X4 and their corresponding logFC for E coil K12 strain under different conditions. X1, X2, X3 and X4 are gene IDs. May you please advise/provide me with codes I can to use to generate a concatenated vector of entrez gene id ...
dep enrichgo bioconductor R clusterprofiler written 3 days ago by tpm10 • updated 3 days ago by Kevin Blighe59k

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