User: ioannis

gravatar for ioannis
ioannis20
Reputation:
20
Status:
New User
Location:
Last seen:
3 months ago
Joined:
1 year, 4 months ago
Email:
i*********************@nord.no

I am a PhD student in Norway and I am working on epigenetics of fish domestication.
Previously I was working mainly with population genetics and microsatellites.
Currently, I am trying to improve my knowledge in bioinformatics and NGS data analysis.

Posts by ioannis

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Count number of characters in every row of a column
... Yes exactly. Thanks a lot Friederike! ...
written 3 months ago by ioannis20
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Comment: C: Count number of characters in every row of a column
... Yes I will import my files into R using read.table(..., stringsAsFactors=FALSE) this will do the job. Thanks a lot Ram. ...
written 3 months ago by ioannis20
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Count number of characters in every row of a column
... Hi community, I was wondering if anyone can give any advice on this: > Chr = c("NC1", "NC2", "NC3") > Pos = c(150, 165, 190) > Seq = c("GATCGATGAC", "GATG", "ACGTAG") > df = data.frame(Chr, Pos, Seq) > df Chr Pos Seq 1 NC1 150 GATCGATGAC 2 ...
R written 3 months ago by ioannis20 • updated 3 months ago by Ram17k
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Comment: C: Finding motifs across a genome
... It runs like a dream! Thanks a lot Bastien! Cheers, Ioannis ...
written 3 months ago by ioannis20
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Finding motifs across a genome
... Hi community, I would like to find the genomic coordinates of all the CCGG motifs across my reference genome. The only thought to go around this would be to `grep` for CCGG across my reference genome and export these sequences in a fasta format. Then align to the same genome and get the coordinates ...
genome ccgg written 3 months ago by ioannis20 • updated 3 months ago by Bastien Hervé1.7k
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Comment: C: NA values of count matrix in class DESeqDataSet
... > rse_gene <- data.frame(c(1,2,3,4,5), c(1,2,3,4,5), c(1,NA,3,4,5), c(NA,NA,NA,4,5), c(1,2,3,4,5)) > colnames(rse_gene) <- c("a","b","c","d","e") > rse_gene[(is.na(rse_gene))] <- 0 > rse_gene a b c d e 1 1 1 1 0 1 2 2 2 0 0 2 3 3 3 3 0 3 4 4 ...
written 10 months ago by ioannis20
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Model matrix for limma voom
... Hello community, I have a large data set called "DWsub". It looks like this: > head(DWsub, n=3) CDx CWx D53x D63x D66x D68x D70x D72x W53x W63x W66x W68x W70x W72x NC_013663.1-295 10 6 125 699 73 48 69 3 307 29 13 33 5 34 ...
limma model.matrix written 10 months ago by ioannis20 • updated 10 months ago by andrew.j.skelton735.2k
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Comment: C: Mapping chromosome locations to gene IDs
... Thanks for the advice. I will have a look at bedtools manual. ...
written 10 months ago by ioannis20
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Mapping chromosome locations to gene IDs
... Hello community, I have a data set (.txt format) that consists of chromosomes and locations like this for example: NC_031974.1- 35234789 NC_031974.1 - 32458 NC_031972.1 - 458920 ... ... ...etc All these unique regions are significantly differentiated between my sample groups. My final goal i ...
gene chromosome coordinates mapping written 10 months ago by ioannis20 • updated 10 months ago by Jean-Karim Heriche16k
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Comparison of Read Count per Genomic Position in R
... Hello community, I have been working for a few months with the data analysis of my sequenced reads in R. Each sample is a different count matrix. Each matrix contains 3 columns (Chromosome, Genomic Position, Read Counts). The rows are more than 400.000 and each row represents a methylated CpG site. ...
R next-gen rna-seq sequencing written 12 months ago by ioannis20

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