User: bioinfo8

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bioinfo8100
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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 4 months ago by bioinfo8100
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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 4 months ago by bioinfo8100
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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 4 months ago by bioinfo8100
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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 4 months ago by bioinfo8100
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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 10 months ago by bioinfo8100
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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 10 months ago by bioinfo8100
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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 12 months ago by bioinfo8100 • updated 12 months ago by Kevin Blighe33k
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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 12 months ago by bioinfo8100
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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 12 months ago by bioinfo8100
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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 12 months ago by bioinfo8100 • updated 12 months ago by Guangchuang Yu2.0k

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Popular Question 10 weeks 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 4 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 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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