User: Nik dAK

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Nik dAK10
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1 month, 3 weeks ago
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1 year, 7 months ago
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n********************@yahoo.com

Posts by Nik dAK

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Variation between technical replicates (DESeq2, batch effects)
... Thank you very much, this is very helpful! ...
written 7 weeks ago by Nik dAK10
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Variation between technical replicates (DESeq2, batch effects)
... Hi all, I read a lot about testing on datasets with batch effects, but in all cases the effect is on biological replicates and not technical replicates. Just some quick terms for a better understanding: technical replicates: same sample, same RNA isolation and same library prep, just loaded 2x on ...
rnaseq deseq2 differential expression batch effect replicates written 8 weeks ago by Nik dAK10 • updated 8 weeks ago by Michael Love26k
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Comment: C: Gviz (GenomicInteractions) arc height and boundaries
... Hi Liz, thank you for the answer. Unfortunately I can't modify the track parameters in any way. stackHeight and other parameters can not be predefined in InteractionTrack() and if I add them manually they are ignored: hic.track@dp@pars$stackHeight <- 0.5 Any suggestions? Thanks ...
written 5 months ago by Nik dAK10
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Gviz (GenomicInteractions) arc height and boundaries
... Hi everybody, I am currently start working with Gviz (thanks for the amazing package), but have a small issue with the interaction track: I use makeGenomicInteractionsFromFile() and InteractionTrack() on a bedpe file. Everything works fine, but the arcs are squeezed against the top border (see ima ...
gviz genomicinteractions written 6 months ago by Nik dAK10 • updated 6 months ago by liz.ingsimmons140
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Comment: C: Rsamtools v 1.99.6 installation error
... Also works for me, thank you very much! ...
written 6 months ago by Nik dAK10
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Comment: C: Rsamtools v 1.99.6 installation error
... scPipe without rtracklayer also works perfectly for me. here is my output of ldd Rsamtools.so after the failed installation: https://pastebin.com/PN3Lmmbv Thanks! ...
written 6 months ago by Nik dAK10
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Comment: C: Rsamtools v 1.99.6 installation error
... you can find my full logs here: https://pastebin.com/fNw41s80 ...
written 6 months ago by Nik dAK10
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Comment: C: Rsamtools v 1.99.6 installation error
... Having the same issue. > BiocManager::install("Rsamtools") Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) ... (some warnings but should be fine) installing to /home/rad/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rsamtools/00new/Rsamtools/libs ** R ** ...
written 6 months ago by Nik dAK10
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rtracklayer::liftOver parameters (minMatch)
... I have a question regarding the parameters available at the command line version but not in R. Is there a possibility to for example alter the minMatch value (Minimum ratio of bases that must remap)? Apparently this value adapts automatically from 0.95 default to 0.1 when using a chain for differe ...
rtracklayer parameters liftover minmatch written 19 months ago by Nik dAK10 • updated 19 months ago by Michael Lawrence11k

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