User: owenchapman1

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Posts by owenchapman1

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Answer: A: Biostrings install error
... filexp_tell is a new function in the latest (Sept 30 2018) version of XVector.  Somehow I had gotten v0.22.0 of XVector, without getting all of the actual updates (my /usr/local/lib/R/site_library/XVector/include/XVector_interface.h file did not have filexp_tell ), but because the version number was ...
written 10 months ago by owenchapman10
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Biostrings install error
... Haven't seen other posts with useful solutions for similar errors, so making a new post.  Trying to install Biostrings using BiocManager, which breaks.  Looks like gcc is throwing a warning on a function called filexp_tell (no mention of it on google...), which eventually prevents loading of the pac ...
biostrings install error written 10 months ago by owenchapman10
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[Deseq2] Estimating size factors using samples which have been excluded for QC
... I'm running analysis of a small number of samples using RNA-seq and ATAC-seq, which produce reads mapping to genes and open chromatin, respectively.  I use DESeq2 to estimate scaling factors for each sample, so that I can compare e.g. the number of reads for region r in sample A to region r in sampl ...
deseq2 estimatesizefactors written 10 months ago by owenchapman10 • updated 10 months ago by Ryan C. Thompson7.4k

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