User: bioinfo8

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bioinfo8120
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Posts by bioinfo8

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Comment: C: Convert gff3 to gtf with R or shell
... Thanks, but I got with -F option in gffread. ...
written 13 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 13 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 13 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 13 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 20 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 20 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 21 months ago by bioinfo8120 • updated 21 months ago by Kevin Blighe48k
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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 22 months ago by bioinfo8120
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Comment: C: Error while running clusterProfiler
... Thanks for the hint. I managed to solve. But now, getting another error from the same command [Guangchuang Yu][1] : Error in validObject(.Object) : invalid class “groupGOResult” object: invalid object for slot "gene" in class "groupGOResult": got class "data.frame", should be or extend c ...
written 22 months ago by bioinfo8120
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Error while running clusterProfiler
... Hi, I am trying to run clusterProfile after installing all dependencies and when I run: ggo <- clusterProfiler::groupGO(gene = gene, OrgDb = org.db, ont = "BP", level = 3, readable = TRUE) I get the following error: Error in rsqlite_send_query(conn@ptr, statement) : external po ...
R clusterprofiler rna-seq written 22 months ago by bioinfo8120 • updated 22 months ago by Guangchuang Yu2.2k

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Popular Question 11 months ago, created a question with more than 1,000 views. For percentage of amino acids, normalize by background amino acid probability
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Popular Question 13 months ago, created a question with more than 1,000 views. For percentage of amino acids, normalize by background amino acid probability
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