User: vasilislenis

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vasilislenis100
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Posts by vasilislenis

<prev • 61 results • page 1 of 7 • next >
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Comment: C: How to extract specific columns from Drugbank xml file
... Many thanks, Pierre for your help! I found Samuel's approach a little bit more complicated since you have to install GO language, so followed your approach by tweaking a little bit the xslt template from your example. I would really appreciate it if you could take a look at it and tell me your thou ...
written 23 days ago by vasilislenis100
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How to extract specific columns from Drugbank xml file
... Hello everyone, I would like to generate a tab-separated file from DrugBank that will include the following tags: I have tried to use the xmlstarlet tool by following Lyco's instructions from here: https://www.biostars.org/p/8400/ but I don't have any result. xmlstarlet doesn't return anyt ...
xml drugbank written 4 weeks ago by vasilislenis100 • updated 4 weeks ago by Pierre Lindenbaum114k
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Comment: C: Downloading and extracting DrugBank data using R
... Hi Kevin, I'm terribly sorry for bothering you with this old post, but I have the same problem and by following the link that you gave I can see that you can download the csv files with the drug name and the protein that correspond but I was wondering if you can have an information about the action ...
written 4 weeks ago by vasilislenis100
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Comment: C: baseline error distribution and missing values
... Thank you very much, Kevin. I can see your point. I will generate each of these functions with the '''na.rm''' option enabled, but what do you mean with the '''stats=function(x)'''? Which will be the '''function(x)'''? The NAs <- 0 is much easier but I believe that I'm missing information with t ...
written 8 weeks ago by vasilislenis100
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baseline error distribution and missing values
... Hi all, I am trying to apply the **LPE** approach on a gene expression set that I have but I have stacked in the calculation of the baseline distribution (I am following the steps that I found on the Bioconductor for the **LPEadj** package) . I am trying to run the following command: var.1 &l ...
gene expression lpe transcriptomics written 9 weeks ago by vasilislenis100 • updated 8 weeks ago by Kevin Blighe32k
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How can I build a ranks matrix on pre calculated fold changes with RankProd?
... Hello, Initially, I would like to apologize in advance in case that my question is naive. Here is the thing. I would like to apply a meta-analysis on different gene expression studies based on ranks. I have found the RankProd library that I would like to use, but the problem is that I want to use ...
R bioconductor gene expressions rankprod written 5 months ago by vasilislenis100
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Comment: C: GO tools: no annotation file for my species
... Thank you very much! The only funny thing is that even if I choose to appear gene ID and gene name for sheep genome and gene ID and gene name for human, the output is gene ID (sheep) transcript ID (sheep) gene ID (human) gene name (human), which is not bad, I can extract the column of interest but ...
written 2.3 years ago by vasilislenis100
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Comment: C: GO tools: no annotation file for my species
... Hi Emily, I chose the orthologous "human genes only" as a filter and the "Ensembl gene ID" and "associated gene name" as attributes. the problem is that I have only the list of the IDs and the name of genes and not another column with the list of IDs of the human genes. Thank you very much! ...
written 2.3 years ago by vasilislenis100
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Comment: C: GO tools: no annotation file for my species
... Thank you very much for your quick answer. Yes, it is there. It is a little bit painful since I have to copy/paste my genes (I cannot find somewhere to upload a file with my genes) but I believe that it does my job :) ...
written 2.3 years ago by vasilislenis100
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GO tools: no annotation file for my species
... Hello, I would like to use the Generic ontology term finder (online tool) for a list of genes but at the third step, it asks me to choose the annotation. The problem is that my species (Ovis aries) is not on the list. I have noticed that in several tools the annotation list is limmited in a specipi ...
ensembl go terms written 2.3 years ago by vasilislenis100 • updated 2.3 years ago by EagleEye5.9k

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