User: bioinfo8

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bioinfo8120
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Posts by bioinfo8

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Comment: C: How can I make boxplot for a single gene from one of the contrasts generated by
... I tried for 1 contrast, but I don't know how to proceed further to extract expression values from fit to make boxplot, would you @[https://www.biostars.org/u/20673/] please help: # Identified top 20 genes. library(limma) ...................... fit <- eBayes(fit) df1 <- top ...
written 11 days ago by bioinfo8120
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How can I make boxplot for a single gene from one of the contrasts generated by limma?
... Hi, I am interested to make **boxplots** for top 20 DEGs (20 separate images) from each of the 5 contrasts. My input data is 1-colour Agilent microarray and I have used `limma`. I could not find any function equivalent to `plotCounts` from `DESeq`. Please guide. Thanks. ...
boxplot contrasts limma microarray written 11 days ago by bioinfo8120 • updated 4 days ago by Gordon Smyth1.2k
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Comment: C: Convert gff3 to gtf with R or shell
... Thanks, but I got with -F option in gffread. ...
written 16 months ago by bioinfo8120
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Comment: C: Convert gff3 to gtf with R or shell
... Thank you, it worked. :) gffread -E -F -O -T input.gff -o output.gtf ...
written 16 months ago by bioinfo8120
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Comment: C: Convert gff3 to gtf with R or shell
... I have modified it before posting, but format is same. :) No, I did not try that. I used: gffread -E -O -T input.gff -o output.gtf ...
written 16 months ago by bioinfo8120
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Convert gff3 to gtf with R or shell
... Hi, I have gff3 file in the following format: #gff-version 3 ##sequence-region Chromosome 1 #!genome-build European Nucleotide Archive #!genome-version #!genome-date 2014-10 #!genome-build-accession #!genebuild-last-updated 2014-10 Chromosome European Nucleoti ...
gff3 R ngs shell gtf written 16 months ago by bioinfo8120
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Comment: C: Fundamentals Of Designing Biological Databases?
... [Jean-Karim Heriche][1] I would like to store information on a protein family among different organisms including their names, gene information, sequence information, structure etc. Would you please elaborate more on access pattern? [1]: https://www.biostars.org/u/2318/ ...
written 22 months ago by bioinfo8120
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Answer: A: Fundamentals Of Designing Biological Databases?
... Hi all, I am looking for ways to create a biological database. I have some data in MS-Access and kind of confused on which approach I should follow to create database. I would like to have an updated opinion from the biostars community on the different ways of creating a database, front and back-en ...
written 22 months ago by bioinfo8120
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Extract gene ids from DESeq2 result dataframe for specific comparison based on vennDiagram
... Hi everyone, I have used the code mentioned [here][1] to generate Venn diagram from `DESeq2` pairwise analysis. 1) I can see 124 genes specific to OPvsLL.33 from the venn diagram (Figure 2) and would like to extract them from DESeq2 result dataframe (already annotated with ensembl) by using entrez ...
venndiagram deseq2 limma rna-seq venn written 2.0 years ago by bioinfo8120 • updated 24 months ago by Kevin Blighe52k
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Comment: C: Error while running clusterProfiler
... I figured out and it worked: gene_char <- as.character(gene$entrezgene) ggo <- clusterProfiler::groupGO(gene = gene_char, OrgDb = org.my_species.eg.db, ont = "BP", level = 3, readable = TRUE) ...
written 2.0 years ago by bioinfo8120

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