User: Farbod

gravatar for Farbod
Farbod3.0k
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Toronto
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s**********@yahoo.com

Hi, I love Biology and Genetics and I have done my PhD thesis on "sturgeon fish RNA-seq" as my MSc was in aquaculture. I am interested in miRNA and epigenetics, too. And having about 4 years of experience in the field of bioinformatics. 

Posts by Farbod

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Answer: A: How to remove Bad Nucleotides represented by "N" from FASTA file by using UNIX?
... Dear @*The Bright Star*, Hi and welcome to Biostars Have you checked the [FASTA cleanup][1] by Pierre Lindenbaum in Biostars? And also "[How to remove N from fasta sequences][2]"? [1]: https://www.biostars.org/p/127714/ [2]: http://seqanswers.com/forums/showthread.php?t=26665 ...
written 6 weeks ago by Farbod3.0k
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Comment: C: Showing FDR and log2FC in Volcano plot using R
... Hi @cpad0112, I have another question and SORRY if it is not a bioinformatic one, Is there any way to **change** these red and blue **colours of dots** (e.g into red and green)? as I could not guess which part of my R script is resbomsible for that by looking at it's line of command. Thanks ...
written 6 weeks ago by Farbod3.0k
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Comment: C: Showing FDR and log2FC in Volcano plot using R
... Hi, I tried it, The blue spots change to red and red dot changed to blue! ...
written 6 weeks ago by Farbod3.0k
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Comment: C: Showing FDR and log2FC in Volcano plot using R
... Yes, In original research I used FDR = 0.001 and log2FC =2 and I want to draw same volcano. but when I set the threshold as "`data$threshold = as.factor(data$-log10(FDR) < 0.001)` " it says :"Error in eval(expr, envir, enclos) : object 'threshold' not found" when I use "`data$threshold = as ...
written 6 weeks ago by Farbod3.0k
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Comment: C: Showing FDR and log2FC in Volcano plot using R
... Thanks, In "aes(x=logFC, y =-log10(FDR)" I should use FDR or -log10(FDR) ? ...
written 6 weeks ago by Farbod3.0k
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Showing FDR and log2FC in Volcano plot using R
... Dear Biostars, Hi In order to bioinformaticly show DEGs of RNA-seq in a volcano plot, I intend to use R, showing DEGs with **blue** spots and not significantly expressed genes with **red** dots. The edgeR package which is embedded in Trinity software, uses **FDR (>0.001)** and log2FC (>2) ...
R rna-seq volcano written 6 weeks ago by Farbod3.0k • updated 6 weeks ago by cpad01124.1k
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Comment: C: Cytoscape network of upregulate and downregulate transcription factors: how to d
... Hi, I also found this topic helpful: [GeneMANIA in Cytoscape][1] [1]: https://www.biostars.org/p/182714/ ...
written 6 weeks ago by Farbod3.0k
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Comment: C: Cytoscape network of upregulate and downregulate transcription factors: how to d
... Hi, I import it as network and Cytoscape accept that. thanks ...
written 6 weeks ago by Farbod3.0k
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Comment: C: Cytoscape network of upregulate and downregulate transcription factors: how to d
... Thank you Leite for your help, I will use your guidance. Ah, those images are really wonderful, I call it a "**Super-help**"! **Q:** Should I save the string network as "as simple tabular text output .tsv" file? > As Cytoscape did not accept it :( ...
written 6 weeks ago by Farbod3.0k
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Comment: C: How many of the SSR contained transcripts have ORF?
... It seems that I can not use this approach because I have used all isoforms for my Transdecoder ORF determination BUT I have used longest isoforms for each gene for SSR mining. So my .bed file have many more member than my fasta file were used for SSR. So, the number of SSr contained transcripts tha ...
written 6 weeks ago by Farbod3.0k

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