User: Bioinformatician_in_trouble

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Posts by Bioinformatician_in_trouble

<prev • 30 results • page 1 of 3 • next >
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RNA seq and Invitro data not matching
... Hi all, Invitro data shows upregulation of certain genes where as RNA seq analysis shows a positive foldchange for same genes but not significant p value and q value. How can i justify this? ...
rna-seq written 3 days ago by Bioinformatician_in_trouble10 • updated 3 days ago by i.sudbery6.3k
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Are there any computationally identified multi targeted drug which are currently or soon to be in clinical trials?
... I searched online, I don't think so there are any. Wanted to know if anyone knows of any. PS: only interested in Clinical trial. I know there are many studies which have used insilico tool and validated the results in-vitro/in-vivo.Thanks! ...
gene written 7 days ago by Bioinformatician_in_trouble10
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Comment: A: Any web based tool to depict long list of GO terms
... Thank you both for your answers, i will probably go ahead with g:Profiler! ...
written 20 days ago by Bioinformatician_in_trouble10
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Comment: C: Volcano plot help code
... I read using read.csv. I am not sure how to upload the image. could you please tell me? or i can send it to you else where if that is okay with you. ...
written 23 days ago by Bioinformatician_in_trouble10
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Any web based tool to depict long list of GO terms
... hi, How do i show a long list of GO term obtained from STRING analysis in my manuscript?I sure could include it in tabular form but was wondering if there are any other ways to show. I have tried REVIGO but the list is so big that REVIGO tree map doesn't come out clear. edit: I understand there is p ...
next-gen rna-seq written 23 days ago by Bioinformatician_in_trouble10
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Comment: C: Volcano plot help code
... `table( as.character(data$GeneId) == 'NA' )` also gives me < table of extent 0 > I was given the csv file with above listed columns, so am not very sure which procedure was used to arrive at the results in csv file. Can we not convert factors into a type that is required by EnhancedVolcano fun ...
written 27 days ago by Bioinformatician_in_trouble10
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Comment: C: Volcano plot help code
... Thank you for your reply,Kevin. table( is.na(as.character(data$GeneId)) ) returns < table of extent 0 > table( is.na(data$GeneId) ) returns < table of extent 0 > I wonder what could the problem outside enhanced volcano be. My input is a csv file with the columns; GeneName, log2 ...
written 28 days ago by Bioinformatician_in_trouble10 • updated 28 days ago by Kevin Blighe51k
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Comment: C: Volcano plot help code
... hi @Kevin Blighe, anything on this please? ...
written 29 days ago by Bioinformatician_in_trouble10
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Comment: C: Volcano plot help code
... Yes, the row names are set. same thing even after trying lab= as.character(data$GeneId). I observed that lot of my rows are NA's for foldchange and qvalue. do you think this is affecting the results? ...
written 6 weeks ago by Bioinformatician_in_trouble10
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Comment: C: Volcano plot help code
... Hi Kevin, This seems like some great package, however I am running into the same "empty plot" error as above. I am pasting the str(data) results of 'data'(i.e. my input file). Could you please let me know,is the file format is wrong? My code for the plot is same as above: EnhancedVolcano(data, ...
written 6 weeks ago by Bioinformatician_in_trouble10 • updated 6 weeks ago by Kevin Blighe51k

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Popular Question 2.0 years ago, created a question with more than 1,000 views. For Detection of fusion from a DNA seq file
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Python Code to standardize gene name in CSV file

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