User: sviatoslav.kendall

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Posts by sviatoslav.kendall

<prev • 65 results • page 1 of 7 • next >
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Bulk downloads from CNGB
... I'm trying to do a bulk download from [CNGB][1] of all the protein sequences they have for a select species. I can find these sequences on their website and know that they number about 30K in total (although at least some are cross-listed on other repositories like Uniprot). But trying to find any o ...
cngb data download repository written 7 months ago by sviatoslav.kendall770
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Comment: C: How can I run a Biopython qblast search targeting a specific set of organisms?
... Thank you so much! Any chance you know how to specify multiple organisms in a single query? Or how to specify that certain taxonomic groups should be excluded? Ultimately, I'm going to want to search within taxonomic groups while excluding specific species... ...
written 8 months ago by sviatoslav.kendall770
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How can I run a Biopython qblast search targeting a specific set of organisms?
... I want to use Biopython's qblast() command to query NCBI's databases but I want to limit my search to specific organisms. Looking at the [documentation for this command][1], I can guess that the "entrez_query" parameter might be helpful but I have not been able to find any information about what sor ...
biopython blast written 8 months ago by sviatoslav.kendall770 • updated 8 months ago by zorbax230
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Comment: C: Align protein in PyMol?
... You can probably find at least some of what you need in [this document][1]. Also: buy a three-button mouse if you haven't already got one - it makes a huge difference when using PyMol. [1]: http://www.pitt.edu/~epolinko/IntroPyMOL.pdf ...
written 9 months ago by sviatoslav.kendall770
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Comment: C: How to calculate TMB for somatic data TCGA
... Count the number of somatic mutations in each sample then divide that number by the length of the sequencing panel used (in megabases). If they were all sequenced using the same protocol, you can probably get away with just counting the number of somatic mutations. If your MAF file contains all the ...
written 9 months ago by sviatoslav.kendall770
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Comment: C: Can't install DESeq2 via Docker container because of dependency issues
... I just got the error message you've posted when trying to run a similarly developed docker image using a command like: docker run Whereas I typically run these sorts of docker images interactively with a command like: docker run -it bash ...and then run an Rscript inside the docker imag ...
written 12 months ago by sviatoslav.kendall770
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Comment: C: Can't install DESeq2 via Docker container because of dependency issues
... Sorry, I haven't got much experience calling R scripts from inside Python and I don't know what to make of that error message either. ...
written 12 months ago by sviatoslav.kendall770
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Answer: A: Can't install DESeq2 via Docker container because of dependency issues
... Try using one of [Bioconductor's own Docker containers][1] as a starting point and then modify the install.R script to include DESeq2 and any required dependencies. Here's an example of a modified Dockerfile and install.R script I made recently that seems to work OK. Dockerfile FROM bioconduct ...
written 12 months ago by sviatoslav.kendall770
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Comment: C: Bioinformatics vs. the Climate Crisis
... > I'll acknowledge that some of my direct responses to the original > poster could have been more diplomatic, And I will acknowledge that I also could have been more diplomatic with you. Sorry about that. Despite our disagreements, I'm much more interested fostering a productive discussion th ...
written 13 months ago by sviatoslav.kendall770
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Comment: C: Bioinformatics vs. the Climate Crisis
... This is really interesting. I agree with a lot of the suspicion and cynicism you've expressed even though I draw some different conclusions than you do. Certainly governments, non-profits and businesses alike have been known to exaggerate and even manufacture crises for the purpose of manipulating t ...
written 13 months ago by sviatoslav.kendall770

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