User: gustavoborin01

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New User
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University of Campinas, Brazil
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2 years, 11 months ago
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4 years, 10 months ago
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Posts by gustavoborin01

<prev • 21 results • page 1 of 3 • next >
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How to randomize my gene network to compare clustering coefficient?
... Hi everyone, I'm trying to create various random networks from my RNASeq gene network (>9.000 nodes) visualized on cytoscape to compare the clustering coefficients, but I don't know how to do this. First, I took a look in the papers seeking for some R package, software or pipeline, but without ...
R cytoscape gene network written 3.0 years ago by gustavoborin0130
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Comment: C: [WGCNA] Error in goodSamplesGenes function
... Did you solve the problem? Probably, you didn't create the object 'gsg' using the goodSamplesGenes function. ...
written 3.0 years ago by gustavoborin0130
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Comment: C: [orthomcl] Proteins with more than one predicted ortholog
... Thank you so much for your help Jean-Karim. It's the first time I've read a good explanation about what is or how can I calculate the normalized score of MCL. ...
written 4.0 years ago by gustavoborin0130
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Comment: C: [orthomcl] Proteins with more than one predicted ortholog
... @Jean-Karim: Thank you for your answer, but the only explanation in this paper is "a normalized similarity score" and it is recommended to see the Orthomcl Algorithm Document for the normalization function. I saw this document (https://docs.google.com/document/d/1RB-SqCjBmcpNq-YbOYdFxotHGuU7RK_wqxqD ...
written 4.0 years ago by gustavoborin0130
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[orthomcl] Proteins with more than one predicted ortholog
... Hi everyone, I have found the predicted orthologs for two fungi through orthomcl algorithm, but when I look at the output table many of the proteins of one fungal have more than one hit and the same occurs for the other fungal. How can I say one protein has two orthologs in the other fungal, or onl ...
orthologs orthomcl evalue written 4.0 years ago by gustavoborin0130 • updated 4.0 years ago by Jean-Karim Heriche20k
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(Closed) [perl modules] Error in perl modules installing
... Hi everyone, I'm trying to find the orthologs between two organisms through orthomcl tool, but I can't not install the DBI and DBD modules from perl in my VM. I've already installed perl (v5.20.1) on my linux ubuntu, but when I try to install the modules, I have the errors below. Actually, I'm foll ...
perl mysql orthomcl dbi written 4.1 years ago by gustavoborin0130
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Comment: C: [WGCNA] Error in goodSamplesGenes function
... Hi, sharanya.ravi. Yes, I've solved it but first let me tell you how my data input looked like. I had a table with my conditions in 7 columns and my experiment's fungal genes in the rows (more than 9,000 genes/rows). So, I run this commands below and it worked. rpkm=read.csv("file.csv",header=T ...
written 4.2 years ago by gustavoborin0130 • updated 6 months ago by Kevin Blighe45k
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Comment: C: [NOISeq] Error in noiseqbio - filter out low counts
... Thank you so much, Komal. Your script code has worked now with me. I really appreciate your answers. I was wondering now if I will have to run this script for each duplicate biological I have to exclude the low counts. If yes, I think the filtered.data function it is more appropriate, don't you agre ...
written 4.4 years ago by gustavoborin0130
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Comment: C: [NOISeq] Error in noiseqbio - filter out low counts
... Komal, I was reading again the NOISeq tutorial and I was thinking if it's really necessary apply this function because there is filtered.data function too which looks like have the same or similar function than noiseqbio. Have you ever used this function? filtered.data(dataset, factor, norm = TRUE, ...
written 4.4 years ago by gustavoborin0130
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Comment: C: [NOISeq] Error in noiseqbio - filter out low counts
... Right.  head(myfactors)   condicao replicas 1     F24h   F24h_1 2     F24h   F24h_2 3      C6h    C6h_1 4      C6h    C6h_2 5     C12h   C12h_1 6     C12h   C12h_2 ...
written 4.4 years ago by gustavoborin0130

Latest awards to gustavoborin01

Popular Question 3.8 years ago, created a question with more than 1,000 views. For [WGCNA] Error in goodSamplesGenes function
Popular Question 3.8 years ago, created a question with more than 1,000 views. For How can I export featureCounts (Rsubread) results?

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