User: rimgubaev

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rimgubaev70
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Posts by rimgubaev

<prev • 18 results • page 1 of 2 • next >
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Is it possible to make a PCA plot for samples using TPM exprssion values in R?
... I have a table with TPM expression values for several samples (10-12) and I want to create PCA plot in order to estimate similarity of raplicates of a certain conditions. If it possible could you please suggest some pipelines or commands for R? ...
pca tpm rna-seq written 12 days ago by rimgubaev70 • updated 12 days ago by andrew.j.skelton735.3k
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(Closed) Why plant biologists do not explain chosen concentrations of phytohormones used for plant treatment?
... It's not quite a bioinformatics question. Maybe you would suggest some other forum. And if you already faced this problem I would be grateful if you suggest some experimental papers where various concentration of phytohormones (Jasmonic and Salicylic acids are be preferable) have been applied and th ...
phytohormones concentrations written 18 days ago by rimgubaev70
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Why volcano plot has no points in the middle of plot?
... Here is an example of volcano plot produced using edgeR results on DEG analysis. So my question is why there is no values in the middle of plot (indicated by red circle)? ![Volcano plot][1] [1]: https://i.pinimg.com/originals/07/69/3d/07693dfcb3c8fe55fcae39d7caa64239.jpg ...
rna-seq volcano plot written 20 days ago by rimgubaev70 • updated 20 days ago by WouterDeCoster32k
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Comment: C: What is wrong with NCBI's gff file?
... Now it's clear, thanks! ...
written 6 weeks ago by rimgubaev70
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What is wrong with NCBI's gff file?
... This is a part of gff file for *Nicotiana tabacum* (tobacco) genome fasta. I must say that the fact that mRNA, gene, 1st exon and 1st CDS start at the same location (2309) is quite confusing! Any ideas? NW_015787321.1 Gnomon gene 2309 5631 . + . ID=gene43;Dbxref=GeneID:107775605;Name=LOC10777 ...
gff written 6 weeks ago by rimgubaev70
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Answer: A: Are there some ways to extract information in tabular format from text with regu
... Solved this problem! I've written a small python scrip which generates tab-formatted text using Nsite output. Here is the code: import sys import re a = sys.argv[1] # reading of input filename (first argument) b = sys.argv[2] # reading of output filename (second argument) ...
written 6 weeks ago by rimgubaev70
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Answer: A: How to extract all promoter regions in multi-fasta format from genome using GFF?
... Finally, I've solved this problem by combining samtools, bedtools as well as custom R script. The pipline placed into bash script is available [here](https://github.com/RimGubaev/extract_promoters). ...
written 10 weeks ago by rimgubaev70
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Are there some ways to extract information in tabular format from text with regular pattern?
... Hello everyone! I have an output from [NsiteM](http://www.softberry.com/berry.phtml?topic=nsitem&group=programs&subgroup=promoter) which represents a text with promoter analysis results. The text has a regular pattern: 1. QUERY: Gene1 Length of Query Sequence: ...
nsitem promoter analysis text mining written 12 weeks ago by rimgubaev70
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Comment: C: Could somebody suggest free pathway visualization tool for omics data from plant
... Nice one but there are only KEGG maps. ...
written 12 weeks ago by rimgubaev70
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Comment: C: How to search cis-regulatory elemens using promoter multifasta from non-model pl
... I am interested in regulatory elements that may affect gene expression under certain condition. For example the presence of several ABREs (Abscisic acid responsive elements) within promoter region indicate that this gene is likely to be up-regulated under unfavorable conditions or ABA treatment. In ...
written 12 weeks ago by rimgubaev70

Latest awards to rimgubaev

Scholar 6 weeks ago, created an answer that has been accepted. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?

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