User: Alex Nesmelov

gravatar for Alex Nesmelov
Alex Nesmelov110
Reputation:
110
Status:
Trusted
Location:
Last seen:
19 hours ago
Joined:
1 year, 6 months ago
Email:
n*******@gmail.com

Posts by Alex Nesmelov

<prev • 24 results • page 1 of 3 • next >
0
votes
1
answer
195
views
1
answers
Answer: A: Using Limma in R to get log2 fold change data for GSE series data, want to get r
... You can recount transcription for genes from bam files, using htseq2 with '-t gene' option. For the calculated expression data, limma::avereps can average data for transcripts (https://www.biostars.org/p/415292/). I'd prefer the first option. By the way, is '1' really an Entrez gene id? ...
written 12 weeks ago by Alex Nesmelov110
0
votes
2
answers
169
views
2
answers
Comment: C: How to deal with "///" separator in Geo2r when loading data to enrichr
... You're doing such an awesome job of popularizing little-known, but extremely handy tidyverse functions! Thank you so much! ...
written 12 weeks ago by Alex Nesmelov110
0
votes
1
answer
153
views
1
answers
Answer: A: How to get nucleotide sequence of the foxp3 enhancer ?
... You may try http://slidebase.binf.ku.dk/ and https://fantom.gsc.riken.jp/zenbu/ ...
written 3 months ago by Alex Nesmelov110
0
votes
0
answers
103
views
0
answers
Comment: C: find NBCI transcript with longest coding sequence for a list of human genes
... Is it possible to identify unambiguously all the genes using these gene symbols in ncbi search? Perhaps, additional filters like " AND Homo sapiens[Primary Organism] AND refseq[filter]" may be necessary. If it is possible, you may easily download all the sequences for different transcripts and then ...
written 3 months ago by Alex Nesmelov110
0
votes
0
answers
180
views
0
answers
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 3 months ago by Alex Nesmelov110
0
votes
0
answers
180
views
0
answers
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 months ago by Alex Nesmelov110
1
vote
1
answer
434
views
1
answers
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 3 months ago by Alex Nesmelov110
0
votes
1
answer
434
views
1
answers
Comment: C: One sample Wilcoxon test for each boxplot ggplot2
... There should be one p-value for each facet, right? ...
written 3 months ago by Alex Nesmelov110
0
votes
1
answer
434
views
1
answers
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 3 months ago by Alex Nesmelov110
0
votes
1
answer
434
views
1
answers
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 3 months ago by Alex Nesmelov110

Latest awards to Alex Nesmelov

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Extracting strings from the fasta header
Scholar 4 months ago, created an answer that has been accepted. For A: Extracting strings from the fasta header
Teacher 4 months 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: 814 users visited in the last hour