User: manaswwm

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manaswwm110
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Posts by manaswwm

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Comment: C: Programmatically get compounds in ChEMBL from related targets
... have you tried using biomaRt in R? more on this package and examples - https://bioconductor.statistik.tu-dortmund.de/packages/3.3/bioc/vignettes/biomaRt/inst/doc/biomaRt.pdf. ...
written 2 days ago by manaswwm110
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Comment: C: Multiple Sequence Alignment for Full length genomes
... have you considered doing MSA on the multiple specific regions of interest. For example, doing MSA on all annotated protein coding regions in the reference genome against your 1800 genomes? I think the protein coding regions would be smaller than the limit for most softwares, and you can also run th ...
written 14 days ago by manaswwm110
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Comment: C: Merge columns, dplyr
... this is also not super informative, sorry. Roughly speaking - you have 3 columns (for state and time) and you want to merge them into one? and then delete the individual 3 columns? I will make an attempt, lets say your data is in data frame `patient_data` and you want to perform the operations on c ...
written 19 days ago by manaswwm110
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Comment: C: Merge columns, dplyr
... It is not entirely clear for me what you want to do. So if I understand correctly, what you have is the following : id time_to_relapse time_to_transformation p1 001 xx yy p2 002 xx1 yy can you ...
written 21 days ago by manaswwm110
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Comment: C: Fatal Error in Gromacs
... As I have mentioned above, this very possibly means that whichever FF you are using, the .rtp entry of that FF does not recognize HB3 hydrogen atom for ASN residue. Kindly look at the .rtp file of the FF that you are using here. You will have to investigate the corresponding entry to HB3 in your FF ...
written 26 days ago by manaswwm110
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Comment: C: biopython entrez lost connection?
... So if I understand correctly, your code works fine for a small subset but not for a larger chunk of ids (lines), so then your code should be technically okay. In your code you are requesting for information from severs (here NCBI). I do not know how biopython does it internally, but these should be ...
written 28 days ago by manaswwm110
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Comment: C: R providing row numbers instead row names with read.csv?
... I am a bit confused on what the dataframe actually looks like, can you do `head(df)` and paste the result here (df is name of your dataframe)? If you mean that there is an additional column which is displaying those rownames (1,2,3..) then have you tried getting rid of it by saying `row.names(df) = ...
written 28 days ago by manaswwm110
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Comment: C: How to use Cytoscape to analyze molecular relationships between genes
... ah, okay. I had imagined that the two values shared between two nodes would be the same, which does not seem to be the case. If I had such "values", the very first thing that I would do in network construction is to use these values as weights of my edges to visualize if the network has any clusters ...
written 28 days ago by manaswwm110
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Comment: C: How to use Cytoscape to analyze molecular relationships between genes
... so if I understand this correctly, for every gene you have values in between this gene to all other genes. One possibility that I can think on the top of my head would be to make these "values" as the weights of your edges? For the purpose of visualization, you can use these "weights" to construct a ...
written 29 days ago by manaswwm110
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Comment: C: Ensembl ID to ENTREZ best converter
... I use biomaRt (for ensembl to uniprot id conversion) and this works fine for me (not 100%, I still loose some ids, but this number is small). Maybe you could try to play around a bit with the "attributes" and "filters"? ...
written 29 days ago by manaswwm110

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Teacher 15 months ago, created an answer with at least 3 up-votes. For C: network visualization (multiple data source integration)

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