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Recent Replies
Answer: Gene enrichment analysis of prokaryotes gene
by
dthorbur
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[Here](https://github.com/golden75/prokaryote_RNASeq) is a tutorial on how to use the R package DESeq2 for prokaryotic RNAseq analyses.
[H…
Comment: Read block operation failed with BAM file
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John Marshall
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Indeed, though it is a seek issue when accessing files over HTTP and other network protocols. So, unless there's something you didn't menti…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
RM123
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Thank you for your help. I am comparing 4 groups, but as I have gene expression data I have a considerable number of boxplots to make. I fo…
Comment: gene correlations in between two groups
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ATpoint
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And how should I know this? I cannot read minds, nor see your screen, data or anything. Please ask a good question with necessary details.
…
Comment: gene correlations in between two groups
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edus_bioinfo
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Thanks. But they are already analyzed. Afaik it analyzes raw data. In my dataset for each gene there is score. I want to interpret the data…
Answer: GWAS phenotype
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dthorbur
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Hello again.
Yes, you can conduct GWAS using binary trait data, but it comes with a whole suite of complications. See [this](https://ww…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
RM123
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Hello Dariober,
That seems like a good solution, however I'm pretty new to R. Could you tell me how I can do that?
Comment: how to create a loop in R
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Nicolas Rosewick
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Not really a bioinformatics related question. Start by looking at R tutorial, there is plenty of them online e.g. : https://www.statmethods…
Comment: Violin plot (Monocle 3) - Troubleshooting
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fracarb8
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You did not add the screenshot.
Answer: BED files
by
Alex Reynolds
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Generically via `bedmap`:
```
bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed
```
The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
dariober
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It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files
by
barslmn
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1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors
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Alex Reynolds
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Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file
by
Alex Reynolds
35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
Comment: Merging the filename with tsv files for master file
by
barslmn
★
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Could you add samples from your files and your expected output.
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