User: Expe

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Expe10
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Posts by Expe

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Answer: A: LEADING and TRAILING in TRIMMOMATIC
... I think that with the leading option you only remove a few nucleotides at the beginning of the reads and keep the rest. The trailing option does the opposite: it removes the nucleotides at the end of the read. [This][1] site and [this][2] site explain why nucleotides should be removed from the begin ...
written 9 months ago by Expe10
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How are the p-adjusted values calculated with the compareCluster function in R?
... Hi everyone, I am trying to do an enrichment analysis with R and compare two protein sets. I have used the compareCluster function from the clusterProfiler package. The plot of my results looks like this [image][1] (I got it from the clusterProfiler vignette). The color code indicates the p-adjust ...
R clusterprofiler comparecluster p-adjusted written 10 months ago by Expe10 • updated 10 months ago by dppb0570
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Is it possible to select the active interaction source in R STRINGdb package like in the website?
... In the Stringdb [website][1] it is possible to select the active interaction sources in settings. Among these options, let's say I am only interested in Experiments and Databases. There I can uncheck the options I don't want. I wonder if this option is available also for R STRINGdb package. The func ...
R interaction stringdb source written 11 months ago by Expe10
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Comment: C: MA plot interpretation before and after normalization
... Sorry for my late reply. The X label is logCPM and the Y label logFC (tumor-control). ...
written 22 months ago by Expe10
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MA plot interpretation before and after normalization
... I have a RNA-seq dataset of tumor and control samples. I plotted two MA plots, before and after normalization (plotSmear with Bioconductor). I don't understand how to know it the results are ok just by looking at the shape. My professor explained that if the 'dot cloud' has a trumpet shape, it is go ...
interpretation ma-plot explanation rna-seq written 22 months ago by Expe10 • updated 22 months ago by YaGalbi1.4k
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Different length but same sequence (PDB)
... Hi, I started working with PDB files and Biopython. I can't figure out why there is a different sequence length between data in fasta files and in pdb files. An example is the protein 5dj7. In the fasta file, the length is 230, whereas in the pdb file, I get 593. To find the length using the pdb fi ...
pdb fasta sequence biopython length written 2.0 years ago by Expe10
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Progress bar to measure blast running time?
... Hello, I wonder if it is possible to use a progress bar (or percentage) to measure the time it takes blast to run in my python script. If so, how to do it? I would like it to appear in the terminal so that the users of the script know that it is going to take time and they don't desperate. What I ...
biopython blast progressbar written 2.0 years ago by Expe10 • updated 2.0 years ago by st.ph.n2.4k

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