User: theobroma22

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theobroma221.0k
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Posts by theobroma22

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Answer: A: How to adjust the position of chromosome or gene labels in OmicCircos
... Did you try adjusting the positions? Did you try setting scale=FALSE in the 330 radius? ...
written 19 days ago by theobroma221.0k
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Answer: A: Is it valid to compare the expression of pre-defined candidate genes from RNA-se
... Just because you observe differences in your candidate genes doesn’t mean they are DE genes. Typically a pre-defined p-value is used as a cut-off to define the DE genes. If your candidates aren’t at least less than or equal to a p-value of 0.5, in your next experiment you could assume a greater p-va ...
written 19 days ago by theobroma221.0k
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Answer: A: edgeR steps for gene expressions
... Something doesn’t seem right to me up top...did you paste all of your code? I could be wrong but where is your “data” object for the “dge” object in: dge = DGEList(counts=cts, genes= rownames(data), group=group)...? ...
written 23 days ago by theobroma221.0k
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Comment: C: Getting interesting gene ontology analysis result
... I personally don’t think the GO results will be interesting, or useful for that matter. Hope this helps. ...
written 5 weeks ago by theobroma221.0k
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Comment: C: Getting interesting gene ontology analysis result
... Since you have the EMBL IDs you can convert them to Entrez IDs, the use the Bioconductor package SPIA, although you will use R. ...
written 5 weeks ago by theobroma221.0k
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Answer: A: Metabolomics log-transform or standardize for WGCNA
... If you can access the mzdata files, the XCMS package on Bioconductor is very handy and thorough! It will annotate your fragments, or you could plug them into WGCNA but I've never did it this way. In XCMS, parse out the highest peak in the peak group and use this as your representative peak for that ...
written 6 weeks ago by theobroma221.0k
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Comment: C: A question about differential expression analysis
... There are so many good tools for scRNA out there to use! ...
written 6 weeks ago by theobroma221.0k
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Comment: C: Difference between genomes in circular graph
... Take care though...Doing all 10 in one circle may be a bit unreadable, hard to interpret. ...
written 6 weeks ago by theobroma221.0k
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Answer: A: Convert gene list to fasta file
... Assuming you have the sequences and you can use R, in R you can use the write.fasta() command which is in the seqinr package. ...
written 6 weeks ago by theobroma221.0k
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Answer: A: plotting interactions in R with two data sets
... I would use a circle plot and have the ribbon thickness represent the strength of the interaction. ...
written 6 weeks ago by theobroma221.0k

Latest awards to theobroma22

Guru 7 weeks ago, received more than 100 upvotes.
Scholar 10 weeks ago, created an answer that has been accepted. For A: Creating a targets matrix
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Creating a targets matrix
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Scholar 4 months ago, created an answer that has been accepted. For A: Creating a targets matrix
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Scholar 7 months ago, created an answer that has been accepted. For A: Creating a targets matrix
Scholar 7 months ago, created an answer that has been accepted. For A: Creating a targets matrix
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Creating a targets matrix
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Scholar 8 months ago, created an answer that has been accepted. For A: Creating a targets matrix
Scholar 8 months ago, created an answer that has been accepted. For A: Creating a targets matrix
Rising Star 8 months ago, created 50 posts within first three months of joining.
Scholar 8 months ago, created an answer that has been accepted. For A: Creating a targets matrix
Scholar 9 months ago, created an answer that has been accepted. For A: Creating a targets matrix
Scholar 10 months ago, created an answer that has been accepted. For A: Creating a targets matrix
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Creating a targets matrix

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