User: sviatoslav.kendall
sviatoslav.kendall • 770
- Reputation:
- 770
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 5 months, 3 weeks ago
- Joined:
- 6 years, 8 months ago
- Email:
- s*****************@gmail.com
Posts by sviatoslav.kendall
<prev
• 65 results •
page 1 of 7 •
next >
0
votes
0
answers
137
views
0
answers
... 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 ...
written 7 months ago by
sviatoslav.kendall • 770
0
votes
1
answer
584
views
1
answers
... 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.kendall • 770
2
votes
1
answer
584
views
1
answer
... 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 ...
written 8 months ago by
sviatoslav.kendall • 770
• updated
8 months ago by
zorbax • 230
0
votes
0
answers
43
views
0
answers
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.kendall • 770
0
votes
1
answer
750
views
1
answers
... 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.kendall • 770
0
votes
1
answer
958
views
1
answers
... 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.kendall • 770
0
votes
1
answer
958
views
1
answers
... 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.kendall • 770
2
votes
1
answer
958
views
1
answers
... 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.kendall • 770
1
vote
3
answers
1.5k
views
3
answers
... > 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.kendall • 770
2
votes
3
answers
1.5k
views
3
answers
... 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.kendall • 770
Latest awards to sviatoslav.kendall
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Commentator
13 months ago,
created a comment with at least 3 up-votes.
For C: Bioinformatics vs. the Climate Crisis
Appreciated
13 months ago,
created a post with more than 5 votes.
For Physical Lab Notebook for Computational Work
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Student
18 months ago,
asked a question with at least 3 up-votes.
For Physical Lab Notebook for Computational Work
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Good Question
2.7 years ago,
asked a question that was upvoted at least 5 times.
For How can I learn cluster computing?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Where can I find more Cancer Datasets for Validation purposes
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For TCGA data looks different on ICGC
Popular Question
3.0 years ago,
created a question with more than 1,000 views.
For TCGA data looks different on ICGC
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For TCGA data looks different on ICGC
Popular Question
3.3 years ago,
created a question with more than 1,000 views.
For TCGA data looks different on ICGC
Good Question
3.5 years ago,
asked a question that was upvoted at least 5 times.
For How can I learn cluster computing?
Popular Question
4.1 years ago,
created a question with more than 1,000 views.
For TCGA data looks different on ICGC
Popular Question
4.3 years ago,
created a question with more than 1,000 views.
For Physical Lab Notebook for Computational Work
Popular Question
4.4 years ago,
created a question with more than 1,000 views.
For How can I learn cluster computing?
Appreciated
4.6 years ago,
created a post with more than 5 votes.
For How Successful are new Bioinformatics Software Companies?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1230 users visited in the last hour