User: Thomas Sandmann

gravatar for Thomas Sandmann
Reputation:
70
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Trusted
Location:
USA
Website:
https://www.linkedin.c...
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Google Scholar Page
Last seen:
2 years, 3 months ago
Joined:
4 years, 11 months ago
Email:
t*******@gmail.com

I am a computational biologist and the author of the gCMAP and gCMAPWeb Bioconductor packages.
 

Posts by Thomas Sandmann

<prev • 22 results • page 1 of 3 • next >
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RStudio in Bioconductor 3.5 AMI incompatible with R 3.4
... 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 ...
ami rstudio server written 2.3 years ago by Thomas Sandmann • 70 • updated 2.3 years ago by shepherl ♦♦ 1.5k
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Dealing with (blood) contamination in RNA-seq data
... 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 ...
rnaseq limma linear model rna-seq written 2.5 years ago by Thomas Sandmann • 70 • updated 2.5 years ago by Aaron Lun • 24k
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Importing genbank entries for synthetic constructs
... 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) : ...
genbankr written 2.8 years ago by Thomas Sandmann • 70 • updated 2.8 years ago by becker.gabriel • 10
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Empty SQL query result for SRA run
... 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 ...
sradb written 2.9 years ago by Thomas Sandmann • 70
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Comment: C: Copying Amazon Bioconductor AMI to another zone
... Awesome, the aws ec2 copy-image command now works. Thanks a lot for enabling this so quickly! ...
written 2.9 years ago by Thomas Sandmann • 70
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Copying Amazon Bioconductor AMI to another zone
... 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 ...
amazon cloud written 2.9 years ago by Thomas Sandmann • 70 • updated 2.9 years ago by Valerie Obenchain • 6.7k
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Some workflows on the BioC website not shown?
... 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 ...
website written 3.0 years ago by Thomas Sandmann • 70 • updated 3.0 years ago by Martin Morgan ♦♦ 23k
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Source of ribosomal RNA sequences to build rrna_genome index for the HTSeqGenie package
... 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 ...
htseqgenie written 3.1 years ago by Thomas Sandmann • 70 • updated 3.1 years ago by Jens Reeder • 40
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Comment: C: How to initialize a SummarizedExperiment?
... Thanks a lot, Martin - both for the great explanation and for pointing out the bioc-devel list. ...
written 3.3 years ago by Thomas Sandmann • 70
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How to initialize a SummarizedExperiment?
... 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 ...
summarizedexperiment written 3.3 years ago by Thomas Sandmann • 70 • updated 3.3 years ago by Martin Morgan ♦♦ 23k

Latest awards to Thomas Sandmann

Popular Question 2.3 years ago, created a question with more than 1,000 views. For Processing bam files by read group
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Dealing with (blood) contamination in RNA-seq data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Copying Amazon Bioconductor AMI to another zone
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Bioconductor docker images without Rstudio-server?
Teacher 5.0 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 5.0 years ago, has more than 80 characters in the information field of the user's profile.
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