User: jnf3769

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jnf376940
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Posts by jnf3769

<prev • 14 results • page 1 of 2 • next >
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Comment: C: miR KEGG enrichment in Arabidopsis
... I did not need to do alignment or quality control of the sequencing data--it was handed off to me by a legacy researcher and I am more concerned with a qualitative assessment, rather than a quantitative one. I intend to go back and check his work after this to make sure we get the same results, but ...
written 6 days ago by jnf376940
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miR KEGG enrichment in Arabidopsis
... Hello all, I have a list of known miRNA's from an experiment in Arabidopsis (example: ath-MIR166a) and I am looking to find out what biochemical pathways they interact with, with KEGG or reactome.db preferably. I have preformed this analysis in humans several times with no issues. If anybody could p ...
enrichment arabidopsis mir kegg mirna written 6 days ago by jnf376940
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Quick and Dirty Gene Network
... Hello all! I need to whip up a little network, preferably from known interactions, from a list of about 100 genes in Arabidopsis. All I have are the gene names. I don't care so much about up and down regulation right, just want to represent the genes interacting in one way or another--its more for d ...
arabidopsis network interactions gene network written 24 days ago by jnf376940 • updated 23 days ago by vakul.mohanty220
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Generating realistic ABI/AB1 electropherograms for educational purposes
... I was wondering if anyone knew of a method by which to generate electropherograms or abi/abi files for a lab I am teaching. The only reason why I am looking for a slightly more realistic way is because the lab is behind schedule due to some issues with the sequencer. I want the students to use softw ...
sequencing abi education ab1 electropherogram written 12 months ago by jnf376940
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Comment: C: Well-resolved Phylogenetic Dataset
... I have a followup question about the 109 E. coli ST131 strains. In the assemblies (ordered or not), there are multiple nodes per fasta file. Am I right in assuming that that means there are more than one contig per file (that is, the genome was not closed)? ...
written 12 months ago by jnf376940
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Well-resolved Phylogenetic Dataset
... Hello all, I am looking to test an alignment-free phylogenetic tree building algorithm I wrote. It can perform both gene and species trees. I have already tested it on a single gene primate tree, but I need some more data to further characterize the algorithm. I know there is a lot of data on TreeB ...
phylogeny dataset phylogenetics data written 12 months ago by jnf376940 • updated 12 months ago by kloetzl570
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OTU distances and assumptions
... I am working on a support vector machine doing some classification based on microbiomes. I am looking to take the relatedness of OTUs into account via some manner of distance measure, but it needs to be a single value. A distance matrix won't cut it. I have already proven to myself that, for an ingr ...
otu phylogenetics scoring distance clustering written 17 months ago by jnf376940
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Comment: C: Coalescent Tree Building
... Thank you! I found these sources to be helpful. There is a lot of bloat in the literature about people using the models, but not explaining it.  ...
written 17 months ago by jnf376940
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Answer: A: RNA-seq normalization and differential expression
... I'd say normalization is part of differential expression analysis. Depending on the biological context of your data and how you performed the sequencing, you may need to do additional normalization or quality control. Arguably, quality control could be considered part of it too or as a preprocessing ...
written 18 months ago by jnf376940
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Coalescent Tree Building
... I am looking for an understanding of how coalescent methods can be applied to tree-building (specifically the construction of a species tree). I know that programs like BEAST can do the analysis for me, but I have yet to find a simple explanation of how it works specifically in the context of tree b ...
coalescent tree search phylogenetics written 18 months ago by jnf376940 • updated 18 months ago by Brice Sarver2.3k

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Scholar 18 months ago, created an answer that has been accepted. For A: RNA-seq normalization and differential expression

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