User: bio.erikson

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bio.erikson20
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Posts by bio.erikson

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Comment: C: Finding orthologs in a organism with a genome duplication.
... Two problems, The WGD is ancient, many of the duplicated genes have low sequence identity, > 70%. But still have functionally identical roles. And I need to know the human ortholog for both gene copies. ...
written 10 days ago by bio.erikson20
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Finding orthologs in a organism with a genome duplication.
... I'm trying to map human orthologs to the allotetraploid *Xenopus Laevis*. I've tried RBH Blast, and looked at a number of other Ortholog finding softwares; but, they all seem to work on finding a one-to-one relationships. This, is problematic for a Laevis, which has 2 copies of almost every gene. C ...
orthologs genome duplication allotetraploid written 10 days ago by bio.erikson20
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EdgeR: Filtering Counts Relationship to Sigficance.
... When I filter my count data with the code in the user guide, the FDR for all my genes drops to 1.0. But, if I lower the CPM cutoff then my FDR creeps up and start to get significant DE genes. The manual states that the CPM is a user preference. And it would seem to be influenced by the library siz ...
rna-seq edger written 4 months ago by bio.erikson20 • updated 4 months ago by Gordon Smyth980
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Taxonomic ids of all pathongenic/BSL<1 microbes.
... I'm trying to identify any human pathogens in a whole genome metagenome survey of enviromental samples. Is there some list or database of pathogenic microbes? Or list of organisms greater than BSL 1? I have NCBI taxonomy ids from KRAKEN. ...
metagenomics written 13 months ago by bio.erikson20
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Resources for a systems biology approach to multiomics.
... I have been tasked to analyze a rich dataset consisting of transcriptomics, proteomics and metabolomics. I want to take a systems biology approach and explore the data and find some new questions to test. I am new to the field of systems biology, and I am trying to find some resources to help me on ...
systems biology metabolomics written 14 months ago by bio.erikson20 • updated 14 months ago by Dattatray Mongad330

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