User: Alex Nesmelov

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Alex Nesmelov110
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Posts by Alex Nesmelov

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Avoid repetition in script
... I meant actually whether there is one object (list or table) holding the data for different chromosomes. As I understand, ch1_SCPG contains the data for the first chromosome - how did you get this table, by loading some separate file or by filtering some large table with data for all chromosomes? A ...
written 1 day ago by Alex Nesmelov110
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Comment: C: Avoid repetition in script
... Do you have any object containing 'ch1_SCPG'-like pieces, such as dataframe or list? Also, will something else change in iterations in addition to the 'ch1_SCPG'-like piece? ...
written 3 days ago by Alex Nesmelov110
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Comment: C: One sample Wilcoxon test for each boxplot ggplot2
... If so, I can suggest making a table with p-values calculated for the corresponding Sequence_biotype and Knockdown type, then add arbitrary y-axis (log2FoldChange) value higher than its actual values to place p-values on top of the bars (say, 5) and finally add this table to the plot with geom_text(d ...
written 4 days ago by Alex Nesmelov110
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Comment: C: One sample Wilcoxon test for each boxplot ggplot2
... There should be one p-value for each facet, right? ...
written 4 days ago by Alex Nesmelov110
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Comment: C: One sample Wilcoxon test for each boxplot ggplot2
... I guess that the problem arises because stat_compare_means compares all groups against all groups - there are too many values to plot. If you specify ref.group or comparisons, p-values will move to the respective bars. As far as I know, it will require an explicit plotting of compared groups on x-ax ...
written 4 days ago by Alex Nesmelov110
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Comment: C: One sample Wilcoxon test for each boxplot ggplot2
... Hi! An expansion of y axis may help to avoid piling up stat_compare_means() results. Alternatively, results of Wilcoxon test may be added on the plot using ggpubr::stat_pvalue_manual(). In such cases, I compute Wilcoxon using ggpubr::compare_means() - maybe because it is directly compatible with ggp ...
written 4 days ago by Alex Nesmelov110
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Answer: A: Fasta Files - How to search for peptide sequences?
... Hi! If you put sequences of peptides of interest into a vector like `peptides_vector = c("DAIPAVEVFEGEPGNK", "AVFQLLDSMGPSLPIAEYIASLDRPR")` you can do the following: library(tidyverse) upstream_peptides <- map(peptides_vector, function(peptide) { ...
written 6 days ago by Alex Nesmelov110
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Answer: A: R script to download all abstracts of Nature in 2020 from Pubmed
... library(rentrez) paper_ids <- entrez_search(db = "pubmed", "Nature[jour] AND 2020[dp]", retmax = 9999, use_history = T) raw_abs <- entrez_fetch(db="pubmed", web_history = paper_ids$web_history, ...
written 9 days ago by Alex Nesmelov110
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Comment: C: WGCNA heatmap error
... The colorMatrix argument was introduced in labeledHeatmap function starting from WGCNA 1.69. As an option, you may try to use an older WGCNA version. Quick and dirty way to try it is a direct loading of an old labeledHeatmap version (e.g., execution of the function code itself, for example, from htt ...
written 11 days ago by Alex Nesmelov110
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Comment: C: WGCNA heatmap error
... Have you check, whether the dimensions of moduleTratCor are consistent with lengths of xLabels and yLabels? `dim(moduleTraitCor) == c(length(names(MEs)), length(colnames(datTraits)))` ...
written 13 days ago by Alex Nesmelov110

Latest awards to Alex Nesmelov

Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Extracting strings from the fasta header
Scholar 25 days ago, created an answer that has been accepted. For A: Extracting strings from the fasta header
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Extracting strings from the fasta header

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