User: maria2019

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maria201990
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Posts by maria2019

<prev • 73 results • page 1 of 8 • next >
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Which journals accept molecular docking analysis using Autodock vina
... Hi, I am very new to the molecular docking world. I have done virtual screening on some drugs for some special receptors suggesting the best drug that can be used as an inhibitor. I have used ZINC15 data based ligands, PDB files from Protein Data Bank as receptors and Autodock vina for docking, pym ...
journal autodock vina molecular docking ligand written 14 hours ago by maria201990 • updated 14 hours ago by Mensur Dlakic4.2k
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Comment: C: Zinc data base drug ID to drug name convertor
... Thanks for your comment, Mensur. I tried that, however, the output format of csv does not give me the name or any other information (even though I check the "name"). The output format of summary table has the names but it does not get extracted as a csv file. ...
written 8 days ago by maria201990
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Zinc data base drug ID to drug name convertor
... Hi, I have downloaded all FDA approved drugs from ZINC data base, about 1600. Each drug has an ID (e.g. ZINC000000000053, which stands for Asprin). How can I convert a list of IDs to the drug name (e.g Aspring), and get some information about the drug? ...
drug name id to name zinc database written 8 days ago by maria201990 • updated 8 days ago by Mensur Dlakic4.2k
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how to get methylated fragments (CpG regions) for only ONE sample using DMAP
... Hi, I am trying to count CpG regions in one of my samples. I know that I can find DMR using DMAP/diffmeth (below is my code). How ever, I do not know how to find (and count) methylated fragments in only one sample. Any suggestions? diffmeth -G $ref_path -A 40,220 -U 0.05 -N -I 5 -R $sample1 -R ...
methylation dmr dmap cpg written 8 weeks ago by maria201990
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Answer: A: Why the PCA results of PCASamples() from methylkit is different from prcomp()?
... I just realized that transpose=FALSE in PCASamples gives the same results as prcomp. pca <- PCASamples(meth, obj.return=TRUE,transpose=FALSE) pca ...
written 8 weeks ago by maria201990
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Why the PCA results of PCASamples() from methylkit is different from prcomp()?
... I have the 'meth' object for my samples and I wanted to see more PCAs. I realized that PCs from PCASamples are different from what I calculate: **Using PCASamples():** library(methylKit) meth <-readRDS(file="~/files/meth.rds") pca <- PCASamples(meth, obj.return=TRUE) pca$x &g ...
pcasamples multiplepca pca prcomp methylkit written 8 weeks ago by maria201990
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Comment: C: How to generate CpG REGIONs file to run DMR analysis with methylkit?
... Thank you very much for your response. This actually helps majority of problem. More in detail, I am working with Rat. I read DMAP which also calculates DMR. They choose sliding windows of 40-220 bp to identify CpG regions with some special thresholds of coverage. I am trying to see if I can extra ...
written 9 weeks ago by maria201990
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How to generate CpG REGIONs file to run DMR analysis with methylkit?
... I have RRBS data that I have pre-processed using bismark. I wanna analyze DMR using methylkit. However, what I have is CpG calls from bismark methyl call and do not have CpG regions. What package is the best to generate CpG regions so that I can run DMR analysis with methylkit? ** I have done DMC a ...
methylkit dmr rrbs cpg-regions written 10 weeks ago by maria201990 • updated 9 weeks ago by Charles Warden7.6k
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Comment: C: How to plot 2 different symbols in a 3D PCA plot generated by rgl-plot3D
... True! thanks for your comment. I just tried it. The problem with plot3D is that I cannot rotate the generated figure. ...
written 10 weeks ago by maria201990
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Comment: C: How to plot 2 different shapes in 3D PCA plots generated by rgl plot3D
... Thanks for your comment. I just tried plot3D. The problem is that I cannot rotate the generated figure ...
written 10 weeks ago by maria201990

Latest awards to maria2019

Scholar 8 weeks ago, created an answer that has been accepted. For C: What is the best R package to plot eye catching 3D PCA plots?
Scholar 11 weeks ago, created an answer that has been accepted. For C: What is the best R package to plot eye catching 3D PCA plots?
Popular Question 3 months ago, created a question with more than 1,000 views. For Strange MT% in 10X scRNA-seq data analysis
Supporter 6 months ago, voted at least 25 times.

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