User: Raito92

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Raito9240
Reputation:
40
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New User
Location:
Italy
Last seen:
2 months, 2 weeks ago
Joined:
8 months, 2 weeks ago
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Posts by Raito92

<prev • 27 results • page 1 of 3 • next >
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Comment: C: GOplot error - Gene Ontology plot generation errors
... I'm sorry, I re-send this because I thought it was due to the fact I attached a dateset. Maybe there were some rules about uploading external files I had ignored... However, I can see the reason of this, but I thought I could ask because the script calls GOplot. The problem also seems to be about s ...
written 11 weeks ago by Raito9240
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(Closed) GOplot error - Gene Ontology plot generation errors
... Hello, I'm trying to run the Trinity script prepnrunGOplot.pl to get plots after GO enrichment analysis (calculated with analyzediff_expr.pl), comparing two samples previously DE analyzed. It calls the goplot package, but I'm getting errors I can't understand I ran: ./prep_n_run_GOplot.pl --GO ...
gene ontology goplot written 11 weeks ago by Raito9240
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GO enrichment analysis graphs after goseq: any easy solutions?
... Hello everyone! I've performed a differential gene expression analysis through Trinity, as suggested [here][1]. GO enrichment analysis was also performed through the analyze_diff_expr.pl script. The function calls the R package **goseq**, and [as stated here][2], the output looks this way: *Two out ...
go goseq gene ontology go enrichment written 11 weeks ago by Raito9240
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Comment: C: Can't install GOSEQ (dependency problem) on CentOS 7!
... This solved the problem, thank you! ...
written 11 weeks ago by Raito9240
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Can't install GOSEQ (dependency problem) on CentOS 7!
... Hello, I've tried to install the package goseq with: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("goseq") But I get * installing *source* package ‘curl’ ... ** package ‘curl’ successfully unpacked and MD5 ...
goseq R r package written 12 weeks ago by Raito9240 • updated 12 weeks ago by Mike Smith4.0k
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Comment: C: topGO package unable to find library(ALL) and data(ALL)
... Solved, thanks! I used this. BiocManager::install("ALL") ...
written 6 months ago by Raito9240
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topGO package unable to find library(ALL) and data(ALL)
... Hello, I'm trying to use the package [topGO][1] to perform an enrichment analysis on my GO terms, but got stuck at the very beginning... I've installed the most recent version of BioConductor and topGO functions themselves, with the suggested code: if (!requireNamespace("BiocManager", quietly= ...
topgo software error written 6 months ago by Raito9240 • updated 6 months ago by James W. MacDonald52k
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Comment: C: Boxplot function not showing all reads length on x-axis
... Hello, I had already tried what you suggested, and oddly enough the x-axis includes a little more bases.. but it's still far from covering the full length range... In addition, the end part of the graph looks slightly different... I'm going to attach a pastebin file of the first lines of my input ...
written 6 months ago by Raito9240
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Boxplot function not showing all reads length on x-axis
... Good morning to everyone, I'm using the boxplot function as suggested in the [RnaSeqEdgeRQ][1]L to show a summary graph of the quality of my input .FASTQ files, which contain my RNASeq input reads (Go to the Paragraph 'Accuracy of base-calling'). As you can see [in the provided example][2], the x-ax ...
sequencing rsubread reads boxplot fastq written 6 months ago by Raito9240 • updated 6 months ago by Wei Shi3.2k
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Comment: C: Function kegga not working for species other than the conventional ones - Pathwa
... Hello, first of all, thanks for your kind and detailed answer! Yes, you guessed it right, I used the domestic olive tree genomic annotation from the Spanish team you mentioned! I realised later that there is, indeed, a way to relate such genes to the wild olive tree ones, and it is contained in th ...
written 7 months ago by Raito9240

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Supporter 8 months ago, voted at least 25 times.

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