User: Thomas Sandmann
Thomas Sandmann • 60
- Reputation:
- 60
- Status:
- Trusted
- Location:
- USA
- Website:
- https://www.linkedin.c...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 year, 4 months ago
- Joined:
- 4 years ago
- Email:
- t*******@gmail.com
I am a computational biologist and the author of the gCMAP and gCMAPWeb Bioconductor packages.
Posts by Thomas Sandmann
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... Dear BioC team,
I noticed that the current release AMI for Bioconductor 3.5 ships with a version of RStudio server that is not compatible with R 3.4. When RStudio server is started, it displays an error message and the plot viewer is disabled.
This is not a problem caused by R or Bioconductor, but ...
written 16 months ago by
Thomas Sandmann • 60
• updated 16 months ago by
shepherl ♦♦ 830
6
votes
1
answer
844
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1
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... Dear Bioconductors,
I am dealing with a poly-A selected RNA-seq dataset that contains samples collected from the central nervous system of mice treated either with a drug or a control vehicle. The primary goal of the analysis is the identification of differential gene expression associated with dr ...
written 19 months ago by
Thomas Sandmann • 60
• updated 19 months ago by
Aaron Lun • 21k
0
votes
1
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426
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... Dear Gabe,
thanks a lot for making the genbankr package available. Today, I tried to parse a genbank entry for a synthetic DNA molecule, e.g. KR709867.1.
Importing this file by accession failed:
id = GBAccession("KR709867.1")
readGenBank(id)
Error in .normargIsCircular(isCircular, seqnames) :
...
written 22 months ago by
Thomas Sandmann • 60
• updated 22 months ago by
becker.gabriel • 0
0
votes
0
answers
393
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... Dear Jack and Sean,
I have tried to use the SRAdb package to retrieve FASTQ files for study, e.g. run SRR2961981.Unfortunately, I run into an error when I try to retrieve the paths to its FASTQ file:
This command succeeds:
listSRAfile("SRR2961981", sra_con, fileType = "sra")
run s ...
written 2.0 years ago by
Thomas Sandmann • 60
0
votes
1
answers
931
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1
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... Awesome, the aws ec2 copy-image command now works. Thanks a lot for enabling this so quickly!
...
written 2.0 years ago by
Thomas Sandmann • 60
5
votes
1
answer
931
views
1
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... Dear Bioconductor team,
I would like to take advantage of the Bioconductor AMIs in the Amazon cloud that are listed here. As documented, these AMIs only exist in the US-East-1 region. Unfortunately, I can only generate VM instance in another region, e.g. us-west-1.
I tried to copy the AMI into th ...
written 2.0 years ago by
Thomas Sandmann • 60
• updated 2.0 years ago by
Valerie Obenchain ♦♦ 6.6k
1
vote
1
answer
276
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1
answer
... It seems the content of some of the workflows aren't rendered on the Bioconductor website right now, e.g.
http://www.bioconductor.org/help/workflows/annotation/Annotating_Genomic_Ranges/
http://www.bioconductor.org/help/workflows/rnaseqGene/
Can anybody confirm and / or take a look?
Thanks,
Tho ...
written 2.1 years ago by
Thomas Sandmann • 60
• updated 2.1 years ago by
Martin Morgan ♦♦ 22k
2
votes
1
answer
401
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1
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... Hi Jens, hi Greg,
I would like to provide a gsnap genome index to detect ribosomal RNAs via the 'detectRRNA.rrna' config parameter of your awesome HTSeqGenie package. I couldn't find any details on how to generate a suitable index of ribosomal RNAs in the package documentation, though. (The unit te ...
written 2.2 years ago by
Thomas Sandmann • 60
• updated 2.2 years ago by
Jens Reeder • 40
0
votes
1
answers
608
views
1
answers
... Thanks a lot, Martin - both for the great explanation and for pointing out the bioc-devel list.
...
written 2.4 years ago by
Thomas Sandmann • 60
3
votes
1
answer
608
views
1
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... Dear Bioconductor users,
I would like to establish a new S4 class, based on the SummarizedExperiment class from the package of the same name.
I am wondering that the correct way of initializing a SummarizedExperiment is. The SummarizedExperiment method accepts e.g. a matrix and constructs the miss ...
written 2.4 years ago by
Thomas Sandmann • 60
• updated 2.4 years ago by
Martin Morgan ♦♦ 22k
Latest awards to Thomas Sandmann
Teacher
4.0 years ago,
created an answer with at least 3 up-votes.
For A: how to save file on local disk after applying predictCoding() function?
Autobiographer
4.0 years ago,
has more than 80 characters in the information field of the user's profile.
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