User: russhh

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russhh4.8k
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UK, U. Glasgow
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@haematobot
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Bioinformatics etc of leukaemia at University of Glasgow
 

Posts by russhh

<prev • 709 results • page 1 of 71 • next >
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Answer: C: Error while using ComplexHeatmap
... The *NAs* in your data are causing the clustering to fail. If you want clustering, you could either restrict to complete cases or do the clustering over imputed values; then I think you can pass in the cluster object to *ComplexHeatmap* (Can't quite remember TBH) ...
written 1 day ago by russhh4.8k • updated 1 day ago by zx87548.4k
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Comment: C: Extract sequences consecutively from a large fasta files and save in new fasta f
... why did you append `--dry-run` to @cpad0112 s code? Could you retry running the command precisely as it was specified ...
written 10 days ago by russhh4.8k
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Comment: C: Need help in programming?
... It sounds like you understand the processes involved in doing this, but your code is way too complicated. Have a look at the biopython SeqIO webpage: https://biopython.org/wiki/SeqIO . ...
written 10 days ago by russhh4.8k
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Comment: C: Need help in programming?
... Can you be sure there will be the same number of sequences in the two input fasta files each time you run this? Which of the languages that you've labelled this question do you have the most experience with? ...
written 10 days ago by russhh4.8k
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Comment: C: ExpressionSet in the age of tidyverse
... Sorry I never posted my code for doing this kind of stuff. Will update when I've had a look at my package again ...
written 22 days ago by russhh4.8k
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Comment: C: deep learning predict gene expression
... All of the above and more. ...
written 23 days ago by russhh4.8k
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Comment: C: Neuralnet on R
... First you look at the function calls, then the function definitions. See https://cran.r-project.org/web/packages/neuralnet/neuralnet.pdf . `neuralnet(fo, data = iris, linear.output=FALSE)` implies the following arguments: ` hidden = 1, threshold = 0.01, stepmax = 1e+05, rep = 1, startweights = NULL ...
written 6 weeks ago by russhh4.8k
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Comment: C: Multi-factor experiment RNAseq limma-voom
... Could you post the code you used to define both your design matrix and your contrasts, please ...
written 8 weeks ago by russhh4.8k
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Comment: C: ComplexHeatmap break values appear different in the plots
... Could you save your heatmap in an object and print the contents of `my_heatmap@matrix_color_mapping`, please ...
written 9 weeks ago by russhh4.8k • updated 9 weeks ago by ATpoint26k
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Comment: C: Visualize overlap differentially expressed genes of multiple comparisons.
... I tend to extract the collection of significant genes (either defined by F test or by union over the comparisons), plot the log-fold-changes wrt each contrast on a heatmap and indicate singificance for a given contrast with a black/white row annotation (one row annotation for each contrast). Even wi ...
written 9 weeks ago by russhh4.8k

Latest awards to russhh

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question 3 months ago, created a question with more than 1,000 views. For setting up MArrayLM objects for use in RUnit tests
Appreciated 4 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Appreciated 4 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Scholar 6 months ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question 6 months ago, created a question with more than 1,000 views. For setting up MArrayLM objects for use in RUnit tests
Appreciated 7 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Scholar 12 months ago, created an answer that has been accepted. For C: muTect analysis, error
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Popular Question 12 months ago, created a question with more than 1,000 views. For Has the RNA-Seq Atlas website closed?
Scholar 12 months ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 13 months ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 14 months ago, created an answer that has been accepted. For C: muTect analysis, error
Appreciated 14 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets

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