User: Russ

gravatar for Russ
Russ320
Reputation:
320
Status:
Trusted
Location:
Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
Last seen:
13 hours ago
Joined:
3 years, 2 months ago
Email:
r*******@uoguelph.ca

Posts by Russ

<prev • 44 results • page 1 of 5 • next >
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Answer: A: Geom_Bar: fill bars with a color gradient
... The order of the colouring is decided by the order (or, in R speak, the levels) of your factor variable "external_gene_name". By default, factors are ordered in alphabetical order (as shown in the legend). You need to re-level the factor to reflect that the order is based on "norm_count_1". Check t ...
written 14 days ago by Russ320
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Comment: C: How to make this specific "pileup" like plot?
... have you looked at Gviz? ...
written 19 days ago by Russ320
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Comment: C: Need help with R script to edit x-axis of snp density plot
... "scales: Are scales shared across all facets (the default, "fixed"), or do they vary across rows ("free_x"), columns ("free_y"), or both rows and columns ("free")" So try adding a `scales="free_x"` argument to your `facet_wrap` function. ...
written 6 weeks ago by Russ320
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Comment: C: Using Circos plot to visualize RNA-seq data
... You're trying to draw a scatter plot of log2 values of gene expression, correct? Have you looked at [this tutorial][1]? It explicitly defines the format your data should be in. To change colours based on criteria (ie over- or under-expressed) you can create rules, [explained here][2]. [1]: http ...
written 8 weeks ago by Russ320
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Comment: C: Using Circos plot to visualize RNA-seq data
... Maybe it's obvious to others, but what do the different tracks in the figure represent? e.g. What are the dots, and why are they different colours? What are the peaks? What format is your data in? ...
written 8 weeks ago by Russ320
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Answer: C: mRNA Biology Question
... A quick google brought this unreferenced tech note from Qiagen: https://www.qiagen.com/us/resources/faq?id=06a192c2-e72d-42e8-9b40-3171e1eb4cb8&lang=en ...
written 3 months ago by Russ320
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Comment: C: GT (genotype information) in haploid organism has a value of 2 .
... What version of GATK are you using? Did you specify the ploidy of your organism while running the analysis? ...
written 3 months ago by Russ320
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Comment: C: This is a file used in the Circos software. Can someone help me understand what
... Link to the documentation on karyotypes: http://circos.ca/documentation/tutorials/ideograms/karyotypes/ ...
written 3 months ago by Russ320
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Answer: A: index of the residue matched using pairwise2 in biopython
... I took a look at the pairwise2 module but also couldn't find any easy way to obtain the indices of the matches ("|"). I was able to modify the format_alignment method slightly to print a list of indices (that starts at 0) of the pipe operator for this specific example - but I'm not sure how it will ...
written 3 months ago by Russ320
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Answer: A: Difference between FC and LogFC
... I find pictures helpful when thinking about these concepts, so quickly made some visualizations for you. They expand on WouterDeCoster's and h.mon's comments. The figures were made in R using with the following code: #Generate fake data fake <- data.frame("gene" = as.numeric(c(1:50)) ...
written 4 months ago by Russ320

Latest awards to Russ

Appreciated 4 months ago, created a post with more than 5 votes. For A: Difference between FC and LogFC
Scholar 4 months ago, created an answer that has been accepted. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Scholar 5 months ago, created an answer that has been accepted. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Popular Question 6 months ago, created a question with more than 1,000 views. For Allelic association tests for polyploid data
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Scholar 10 months ago, created an answer that has been accepted. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Supporter 11 months ago, voted at least 25 times.
Scholar 12 months ago, created an answer that has been accepted. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Teacher 12 months ago, created an answer with at least 3 up-votes. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]

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