User: Jens Preussner

Reputation:
30
Status:
New User
Location:
Germany
Last seen:
1 month, 1 week ago
Joined:
3 years, 10 months ago
Email:
j*************@mpi-bn.mpg.de

Posts by Jens Preussner

<prev • 8 results • page 1 of 1 • next >
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Comment: C: GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
... Thats great! Thank you for your time and effort. R CMD INSTALL --no-test-load GO.db_... did the trick! Who knows why the .libPaths() are different between installation and run time, but it worked now. Thanks again for your help! Highly appreciated! ...
written 5 weeks ago by Jens Preussner30
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Comment: C: GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
... Thanks for your reply. AnnotationDbi installation is successful, but GO.db fails afterwards with the error message seen above. ...
written 5 weeks ago by Jens Preussner30
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GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
... Hi all, I'm trying to install GO.db on Mac OS X with R3.5.0 and Bioconductor 3.7.0: > library(AnnotationDbi) Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘pac ...
go annotationdbi bioclite mac os x r3.5 written 5 weeks ago by Jens Preussner30 • updated 5 weeks ago by Martin Morgan ♦♦ 22k
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Comment: C: [MnnCorrect] In case of known subpopulations
... Yes, the cells were sourced from the same population and dissociated in the same manner as well. I played around a bit and noticed that the normalization strategy might have an effect. Are there further recommendation for the mnnCorrect input, besides being log2 transformed? Is the log2(counts) as f ...
written 11 months ago by Jens Preussner30
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Comment: A: [MnnCorrect] In case of known subpopulations
... Hi Aaron, thanks a lot for your reply. The time points are not homogeneous populations. We know this from analyzing the full-length cDNA sequencing data alone and we expect the detected (sub)-subpopulations also in the 3'-end-sequencing data. However, analysis of this data alone does not resolve th ...
written 11 months ago by Jens Preussner30
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[MnnCorrect] In case of known subpopulations
... Dear all, dear Laleh and Aaron, I have a "best practice" question regarding the mnnCorrect that you provide in scran. My setup is the following: We sampled single cells from three different time points across two sequencing platforms (3'-end and full-length cDNA). Unfortunately, the sequencing dept ...
rnaseq scran single-cell mnncorrect written 11 months ago by Jens Preussner30
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ChIPpeakAnno: Non-empty IRange object in case of no overlap
... Dear Julie, when using the annotatePeakInBatch function of your ChIPpeakAnno package with non-overlapping peaks and annotation, the resulting object equals the input peaks. Is this intended? How would I know that there is no overlap then? I used a work-around with all(ovl == peaks) to check if the ...
iranges chippeakanno written 3.6 years ago by Jens Preussner30 • updated 3.6 years ago by Julie Zhu3.8k
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ChIPpeakAnno: Invalid row.names length in peaksNearBDP
... Dear Julie, I noticed an unwanted breaking of the peaksNearBDP function in your package. When searching for bidirectional promoters in annotationData that contains just one entry, the function gives an "invalid row.names error". Is this intended? Just for completeness and reproducability, I used t ...
annotation annotationdata written 3.9 years ago by Jens Preussner30 • updated 3.9 years ago by Julie Zhu3.8k

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