User: lplough

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lplough0
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Posts by lplough

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Comment: C: Using Sailfish estimated read-counts for DESeq2 analysis
... OK. So then, what to do if you want correct, gene-level counts from RNAseq data with a de-novo assembly (e.g. Trinity or Bridger) in which there often multiple isoforms for each gene or component, and reads may map multiply to those isoforms?   IS the solution to keep only the longest isoform (or is ...
written 2.7 years ago by lplough0
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Comment: C: how to load edgeR each time I start R?
... Sorry, I didn't explain myself well.  I haven't been using Bioconductor for long, so thought I had missed something in how packages were loaded/retained/accessed.  Anyway I figured out my brainfart.  I was switching between 2 servers and R versions and had not installed BiocLite on both. So I though ...
written 4.3 years ago by lplough0
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how to load edgeR each time I start R?
... This is an easy question but I can't find good documentation.  After installing  or "sourcing" biocLite and installed relevant packages (edgeR, etc) I can run my analyses. But after closing the R session, and then restarting it, I have to resource BiocLite and then load all packages again. Seems li ...
edger bioclite installation written 4.3 years ago by lplough0 • updated 4.3 years ago by James W. MacDonald51k

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