User: lrutter0306

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lrutter030610
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United States
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3 months ago
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4 years, 6 months ago
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Posts by lrutter0306

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Convert Gene IDs into ENTREZ or ENSEMBL format (honey bee / apis mellifera)
... Thanks, Denise. Just checking, but how should I interpret this Error then if it seems I am providing the correct information? ...
written 3 months ago by lrutter030610
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Preparing RNA-seq data for Hierarchical Clustering
... I am clustering RNA-seq data into groups of similar expression patterns and visualizing the results. To this end, I have been: 1) Logging and normalizing the RNA-seq data with the following two methods (first is from edgeR package, second is from EDASeq package) cpm.data.new <- cpm(data, TR ...
rna-seq written 3 months ago by lrutter030610 • updated 3 months ago by Kevin Blighe19k
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Convert Gene IDs into ENTREZ or ENSEMBL format (honey bee / apis mellifera)
... Hello, I am trying to use the getGeneLengthAndGCContent() function from the EDASeq R package to obtain gene lengths and GC content for each gene in a honeybee (apis mellifera) dataset. An example subset of these genes are as follows: "GB40001" "GB40002" "GB40003" "GB40004" "GB40005" "GB40006" ...
ensembl entrez rna-seq written 6 months ago by lrutter030610 • updated 6 months ago by Emily_Ensembl14k
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Comment: C: How is logFC and p-value estimated (for volcano plots)?
... I used a normalized version of my data. Thank you. ...
written 9 months ago by lrutter030610
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How is logFC and p-value estimated (for volcano plots)?
... I am trying to understand how volcano plots are made in DEG studies. Say I have an example data frame that begins with the following first three rows: > head(myDF) ID C_S1_R1 C_S1_R2 C_S1_R3 C_S2_R1 C_S2_R2 C_S2_R3 1 Glyma0002s50.1 4.9191791 5.2691071 4.88150 ...
R foldchange edger written 13 months ago by lrutter030610 • updated 8 weeks ago by jha.barkha80
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Comment: C: Terminology question: Phylogenetic tree duplicated generation counts
... Thank you, David. I see what you mean about me misnaming it as phylogenetic. The visualization that I am thinking of, then, is a visualization of a simple cyclic graph, where the nodes are constrained by edge distance from the root node. Do you think that is the most standardized/eloquent/specific w ...
written 3.4 years ago by lrutter030610
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Comment: C: Terminology question: Phylogenetic tree duplicated generation counts
... Okay, I am editing the question. What I want to know is, what would be an appropriate term to call a visualization of this type of graphical structure, where one axis is constrained to generation count. For example, the root node (node A) is at x=1. Then node B and C are at x =2. Node E is at x=3. N ...
written 3.4 years ago by lrutter030610
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Terminology question: Phylogenetic tree duplicated generation counts
... Say I have a directional tree with the following edges: nodeA --> nodeB nodeA --> nodeC nodeB --> nodeD nodeC --> nodeE nodeE --> nodeD   This means that the following nodes are of the following generations: nodeA = 1 nodeB = 2 nodeC = 2 nodeD = 3, 4 nodeE = 3   What wou ...
phylogeny bioinformatics terminology graph written 3.4 years ago by lrutter030610
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Preparing a .genome file for snpEff
... Hello, I am trying to follow the example code at this site (http://snpeff.sourceforge.net/protocol.html) where snpEFF and GATK are linked together:   java -Xmx4g -jar snpEff.jar \ -v \ -o gatk \ GRCh37.71 \ protocols/ex1.vcf \ > protocols/ex1.eff.gatk.vcf   I have a data.vcf, data.fasta, dat ...
ngs snpeff genomefile written 3.4 years ago by lrutter030610 • updated 24 months ago by sbombin10
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Comment: C: Convert .Gff3 File To 12-Column .Bed File
... As a side note, only other thing I noticed is that the score column (Column 6) of my .gff3 file does not always seem to be a number between 0 and 1000, which is the consensus of what I see online. In fact, 1844/183,748 lines of the .gff3 file have negative values for the score column. I downloaded i ...
written 4.5 years ago by lrutter030610

Latest awards to lrutter0306

Great Question 2.1 years ago, created a question with more than 5,000 views. For Convert .Gff3 File To 12-Column .Bed File
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Convert .Gff3 File To 12-Column .Bed File
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Convert .Gff3 File To 12-Column .Bed File

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