User: biosjm

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biosjm0
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Posts by biosjm

<prev • 19 results • page 1 of 2 • next >
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Comment: C: deseq2 design with two variables
... you mean if I use ~group? ...
written 12 days ago by biosjm0
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Comment: A: deseq2 design with two variables
... What do you mean with full rank message? ...
written 16 days ago by biosjm0
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Comment: A: deseq2 design with two variables
... No within the 3 variables I have 5 replicates ...
written 16 days ago by biosjm0
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deseq2 design with two variables
... Hello, I `ve conducted DEG analysis by Deseq2 and I just want to make sure that I´m right. I have to following information for the design: info: region: region1, region 1, region 2, species: species1, species 2, species1 group: region1_species1, region1_species2, region2_species1 ...
deseq2 design written 17 days ago by biosjm0
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Comment: C: Too many Terms after Enrichment analysis
... Yes, the problem with clusterprofiler is, that you have to use search_kegg_organism, so you have to search for a organism. Due to the fact, that I have a assembly, I have KEGG numbers from several organism. ...
written 4 weeks ago by biosjm0
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Comment: C: Too many Terms after Enrichment analysis
... Thanks, very helpful! Can you recommend a package I can use for KEGG analysis/enrichment? I used TopGO for GO enrichment analysis, but could not find something similar for KEGG. I have already a custom annotation table (de novo transcriptome assembly- containing among others informations of KEGG/KO ...
written 4 weeks ago by biosjm0
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Comment: A: Too many Terms after Enrichment analysis
... Thank you for your answer, ATpoint. Yes, I have set already the threshold for log2foldchange to 1. I have to say, that I have a non model organism and have a custom annotation table containing also KEGG and KO Ids. I made the experience, that many tools/packages are only available for model organism ...
written 4 weeks ago by biosjm0
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Too many Terms after Enrichment analysis
... Hi all, I obtained after DEG analysis with deseq2 and Go enrichment analysis (fisher,classic) with TopGo a long list of enriched terms. They are from several levels and too many (500) to explain all of them. I´m not sure how I should proceed... Is there a slimfunction I can use after using TopGO? ...
slim go enrichment analysis written 4 weeks ago by biosjm0
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TopGO- how to get enriched terms at a specific level?
... Hello, I am working at the moment on RNA seq data of a non model organism and have a list of genes of interest. I`ve done already Go enrichment analysis of DEG with topGO, but the enriched terms are from different levels. Do you know, how to get those GO terms at a specific level (e.g. level 3?) wi ...
topgo go enrichment rna-seq written 8 weeks ago by biosjm0
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Summarize gene functions from sprot_top_blast_hit_P
... Hello, I am working at the moment on RNA seq data of a non model organism and have a list of genes of interest. I`ve done already Go enrichment analysis, but I´m interested also now on the special gene functions listed in my custom annotation table under sprot_top blast_hit_P. Of course I can look ...
gene function rna-seq sprot top blast hit p written 3 months ago by biosjm0

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