User: Alex Nesmelov

gravatar for Alex Nesmelov
Alex Nesmelov110
Reputation:
110
Status:
Trusted
Location:
Last seen:
3 days, 15 hours ago
Joined:
1 year, 3 months ago
Email:
n*******@gmail.com

Posts by Alex Nesmelov

<prev • 24 results • page 2 of 3 • next >
2
votes
1
answer
117
views
1
answers
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 4 weeks ago by Alex Nesmelov110
3
votes
2
answers
171
views
2
answers
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$web_history, ...
written 5 weeks ago by Alex Nesmelov110
0
votes
0
answers
203
views
0
answers
Comment: C: WGCNA heatmap error
... The colorMatrix argument was introduced in labeledHeatmap function starting from WGCNA 1.69. As an option, you may try to use an older WGCNA version. Quick and dirty way to try it is a direct loading of an old labeledHeatmap version (e.g., execution of the function code itself, for example, from htt ...
written 5 weeks ago by Alex Nesmelov110
0
votes
0
answers
203
views
0
answers
Comment: C: WGCNA heatmap error
... Have you check, whether the dimensions of moduleTratCor are consistent with lengths of xLabels and yLabels? `dim(moduleTraitCor) == c(length(names(MEs)), length(colnames(datTraits)))` ...
written 5 weeks ago by Alex Nesmelov110
1
vote
0
answers
152
views
0
answers
Comment: C: Gene expression from cell counts matrix
... Ok! Thank you for the explanation! ...
written 5 weeks ago by Alex Nesmelov110
0
votes
1
answer
162
views
1
answers
Comment: C: Loop to retrieve rsID out of chrID list
... BTW, I do not know whether the list that you passed to getBW as 'values' argument is correct - repeating POS values twice looks counterintuitive to me, but I did not work with biomartr and can't advice on this matter. ...
written 5 weeks ago by Alex Nesmelov110
0
votes
0
answers
152
views
0
answers
Comment: C: Gene expression from cell counts matrix
... ATpoint, I really wonder - do some features of the presented data really provide some clues on it's single-cell origin? Or you guessed just because TS mentioned Seurat? ...
written 5 weeks ago by Alex Nesmelov110
1
vote
1
answer
162
views
1
answers
Comment: C: Loop to retrieve rsID out of chrID list
... At least, you can easily check whether there is some progress adding 'print(head(temp))' after getBM query. Hovewer, in such a loop I would expect some subsetting like SSNP_M_Ch$CHR[i] aimed to feed getBM with a single current value. Presented code looks like whole CHR and POS columns of SSNP_M_Ch a ...
written 5 weeks ago by Alex Nesmelov110
0
votes
2
answers
188
views
2
answers
Answer: A: How to make a gene counts matrix ? (input edgeR/DESeq2)
... You may easily merge all tables, if you'll put them all in a list and then use purrr::reduce function. Try this: library(tidyverse) counts_files_pattern = "\\.csv$" counts_table <- list.files(pattern = counts_files_pattern) %>% #apply an import function to the ...
written 6 weeks ago by Alex Nesmelov110
0
votes
2
answers
172
views
2
answers
Comment: C: Extracting strings from the fasta header
... We are replacing whole string by three values of interest which are matched via parentheses and referred in replacement as \\\\1, \\\\2 \\\\3. The trick is to match somehow a whole string to get rid of it. - ^.*?locus_tag= ------ anything from the start ^ up to locus_tag=, including ...
written 7 weeks ago by Alex Nesmelov110

Latest awards to Alex Nesmelov

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Extracting strings from the fasta header
Scholar 7 weeks ago, created an answer that has been accepted. For A: Extracting strings from the fasta header
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Extracting strings from the fasta header

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 693 users visited in the last hour