User: david.rinker

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david.rinker10
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Posts by david.rinker

<prev • 5 results • page 1 of 1 • next >
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Answer: A: GenomicFeatures and custom genomes?
... Ok, guess this question is a bust.  If the developers are reading, it might be a useful addition to the manual and/or vignette to outline this process. More and more "non-model" organisms are being sequenced and analyzed--those users are inevitably going to want to do what I'm currently trying to d ...
written 5 weeks ago by david.rinker10
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GenomicFeatures and custom genomes?
... Hi I want to use GenomicFeatures to extract upstream sequences from a genome using gene_IDs My organism (Anopheles melas) has an assembled genome (fasta) and a gtf file. It seems like these are all the files I should need, however I am not finding it easy to figure out on how to load these two dat ...
genomicfeatures written 5 weeks ago by david.rinker10 • updated 4 weeks ago by Hervé Pagès ♦♦ 13k
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Comment: C: Does DEseq2 analysis make GOseq redundant?
... Ok.  Thanks to you both for helping to clarify this. Much appreciated! ...
written 4 months ago by david.rinker10
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Comment: C: Does DEseq2 analysis make GOseq redundant?
... Thanks for the response. My language was very imprecise. I meant to ask whether false negatives (in the GO enrichment results)  could be introduced by unnecessarily devaluing longer genes? The way that I understand the paper, GOseq assigns weights based upon size:  "The PWF quantifies how the prob ...
written 4 months ago by david.rinker10
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Does DEseq2 analysis make GOseq redundant?
... I'm running a deferential expression pipeline that first calculates DE with DEseq2 and then looks for enticement in the DE genes. This pipeline seems somewhat common in the literature, so I'm sure it's fine. While well represented in the literature, I'm wondering if this approach is not redundant? ...

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