User: Jens Preussner

Reputation:
10
Status:
New User
Location:
Germany
Last seen:
3 months, 3 weeks ago
Joined:
3 years, 2 months ago
Email:
j*************@mpi-bn.mpg.de

Posts by Jens Preussner

<prev • 5 results • page 1 of 1 • next >
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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 3 months ago by Jens Preussner10
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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 3 months ago by Jens Preussner10
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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 3 months ago by Jens Preussner10
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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 2.9 years ago by Jens Preussner10 • updated 2.9 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 3.2 years ago by Jens Preussner10 • updated 3.2 years ago by Julie Zhu3.8k

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