User: Brian Gudenas

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Posts by Brian Gudenas

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Sleuth Error: System is computationally singular
... The full model should only be testing the effect of condition not Tissue + condition, so you would need to add Tissue to the reduced model. so <- sleuth_fit(so, ~ Tissue, ~ Condition, 'full') so <- sleuth_fit(so, ~ Tissue, 'reduced') ...
written 6 months ago by Brian Gudenas90
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Answer: A: Gene set enrichment analyses of different samples of the same species
... It sounds like you would want to select an FPKM threshold to establish which genes are highly expressed at each life stage. This would give you a gene list for each life stage which you could perform gene set enrichment analysis on using the full peptidase gene list as the background set with a tool ...
written 6 months ago by Brian Gudenas90
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Answer: A: Sleuth Error: System is computationally singular
... Is "sample" just a unique sample identifier?? Then it should not be included as a batch variable and you should drop it from your sleuth_fit call. Also why are you including tissue if they are all from the same tissue, if there is no variability then there is no point in including it as a batch var ...
written 6 months ago by Brian Gudenas90
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Answer: A: Download all files from encode matching filter specifications
... If you go to the ENCODE project experiment matrix webpage here https://www.encodeproject.org/matrix/?type=Experiment You can select all your desired filters (Assay, Organism, data type ) then click the download button on the bottom to get a file containing the links to all desired datasets (1st li ...
written 6 months ago by Brian Gudenas90
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Answer: A: Bulk download introns, exons, and UTR regions from Ensembl for gene prediction t
... Check out the biomaRt R package, specifically the getSequence function which allows you to use a list of gene identifiers (Ensembl, or entrezgene) to retrieve sequences of interest by changing the seqType parameter (cdna, 3utr, 5utr, gene_exon, gene_intron, etc..) library(biomaRt) mart = u ...
written 6 months ago by Brian Gudenas90
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Answer: A: Signed vs unsigned network construction: wgcna issue!
... A scale free topology index of 0.9 or greater is not required for WGCNA, although it should probably be above 0.8 Just take a look at the R code  from this publication (authored by the creator of WGCNA), they use a soft threshold of 26 (signed network) which only achieves an index of  0.808. http: ...
written 2.9 years ago by Brian Gudenas90
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Answer: A: WGCNA for less than 15 samples
... You can make an easy co-expression network by simply constructing the symmetric correlation matrix of all genes (adjaceny matrix as its called in WGCNA) then filtering that matrix by a hard threshold such as r = 0.70. Although, based on your newest comment i am not sure why differential expression ...
written 2.9 years ago by Brian Gudenas90

Latest awards to Brian Gudenas

Scholar 6 months ago, created an answer that has been accepted. For A: Bulk download introns, exons, and UTR regions from Ensembl for gene prediction t
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Bulk download introns, exons, and UTR regions from Ensembl for gene prediction t
Scholar 6 months ago, created an answer that has been accepted. For A: Bulk download introns, exons, and UTR regions from Ensembl for gene prediction t
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Bulk download introns, exons, and UTR regions from Ensembl for gene prediction t

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