User: devarts

gravatar for devarts
devarts20
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20
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New User
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1 month ago
Joined:
4 months, 1 week ago
Email:
d******@uoregon.edu

Posts by devarts

<prev • 17 results • page 1 of 2 • next >
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Answer: A: Biopython not installed correctly error when trying to call python script from R
... What I found is that parts of the Biopython that was being called within the python script, that was being called, were deprecated. Changing those, made it work. ...
written 4 weeks ago by devarts20
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Comment: A: Biopython not installed correctly error when trying to call python script from R
... Dummy Python commands work. What I found is that parts of the Biopython that was being called within the python script, that was being called, were deprecated. Changing those, made it work. ...
written 4 weeks ago by devarts20
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Biopython not installed correctly error when trying to call python script from R on a MacOS
... I'm trying to run a script in r that relies on calling a python script. I'm using a Mac with Python 3.8.2 installed and Biopython installed through Python 3, but I keep getting the following error. I've uninstalled and reinstalled Python 3 and Biopython, but continue to get the following error. "B ...
biopython written 4 weeks ago by devarts20
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Can you do KEGG analysis in R without Entrez I.D.s
... Hi All. I've another newbie question for you. I've done RNAseq analysis in R for a set of organisms of the yeast species Yarrowia lipolytica strain CLIB122, with Ensembl IDs. I'd also like to do some KEGG ontology analysis. The tools that I have used for KEGG and GO analysis in the past (KEGGa (p ...
R biomart entrez rna-seq kegg written 12 weeks ago by devarts20
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Comment: C: Ensembl reference genomes and annotations by chromosome only.
... h.mon, I think that's the ticket. I was uncertain about using the toplevel files. I did see that those are available for my organism. ...
written 3 months ago by devarts20
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Comment: C: Ensembl reference genomes and annotations by chromosome only.
... I didn't have any initial ideas, other than running alignment and feature counting for each chromosome individually and then trying to use deplyr to combine data tables in R, as I was planning on doing the differential expression with EdgeR in R. But, I'll try using awk and shell loops to do this p ...
written 3 months ago by devarts20
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Ensembl reference genomes and annotations by chromosome only.
... Hi All. Ensembl has the reference genome and annotations that I need separated into files by chromosome. I'd like to combine these into one file with an additional column to specify which chromosome they are found on, so that I can align and generate feature counts for the organisms whole genome, ...
ensembl alignment feature counts rna-seq written 3 months ago by devarts20 • updated 3 months ago by h.mon31k
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Comment: C: Rsubread featureCounts returns no matches
... This was the problem. I was, thus able to fix it. Thank You! ...
written 3 months ago by devarts20
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Comment: A: Rsubread featureCounts returns no matches
... Thanks to genomax, I found that my chromosome identifiers were not identical in my reference genome and my annotations file, which led to the problem. I was able to rectify this. ...
written 3 months ago by devarts20
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Comment: C: Rsubread featureCounts returns no matches
... Good question. I'm going to take a look at the files. ...
written 3 months ago by devarts20

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