User: bioinfo8

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bioinfo890
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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 6 weeks ago by bioinfo890
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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 6 weeks ago by bioinfo890
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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 6 weeks ago by bioinfo890
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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 6 weeks ago by bioinfo890
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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 7 months ago by bioinfo890
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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 8 months ago by bioinfo890
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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 9 months ago by bioinfo890 • updated 9 months ago by Kevin Blighe28k
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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 9 months ago by bioinfo890
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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 10 months ago by bioinfo890
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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 10 months ago by bioinfo890 • updated 10 months ago by Guangchuang Yu1.9k

Latest awards to bioinfo8

Popular Question 29 days ago, created a question with more than 1,000 views. For percentage of amino acids, normalize by background amino acid probability
Popular Question 5 weeks ago, created a question with more than 1,000 views. For percentage of amino acids, normalize by background amino acid probability
Popular Question 5 weeks ago, created a question with more than 1,000 views. For percentage of amino acids, normalize by background amino acid probability
Popular Question 7 months ago, created a question with more than 1,000 views. For percentage of amino acids, normalize by background amino acid probability
Popular Question 7 months ago, created a question with more than 1,000 views. For Sleuth: Combined lrt and wt tests, clustered heatmap
Popular Question 10 months ago, created a question with more than 1,000 views. For Sleuth: Combined lrt and wt tests, clustered heatmap
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