User: al-ash

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al-ash10
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Posts by al-ash

<prev • 8 results • page 1 of 1 • next >
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Comment: C: topGO: how to rettrieve (long) GO term description without abbreviating
... Yes, thanks for suggesting the package. I'm now indeed using  Term() function from GO.db package to retrieve terms for ids...I was just wondering if I'm not missing an argument in topGO which would do it directly. ...
written 11 weeks ago by al-ash10
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topGO: how to rettrieve (long) GO term description without abbreviating
... topGO returns in the result table of enriched GO terms GO term descriptions. But longer description is abbreviated with "..." as in the attached part of topGO result table (first two columns of results). Is there a way how to retrieve directly from topGO the non-truncated term descriptions? (I'd lik ...
topgo written 11 weeks ago by al-ash10
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Comment: C: DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq
... Yes, the orthologs have always the same name (name of the orthologous group) across all samples (species). Thanks for clarifying this for me.   ...
written 12 weeks ago by al-ash10
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Comment: C: DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq
... I have 2500 orthologs in each organism. I expect that only relatively small portion will be DE (partly because I do not have biological replicates in sense of multiple RNAseq data from a single species but instead I use phylogenetic replicates - i.e. distinct species which share some characterist ...
written 12 weeks ago by al-ash10
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DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
... Background: I would like to identify differentially expressed gene orthologs across multiple related organisms. I predicted a set of single copy orthologs from transcriptome de novo assemblies and quantified expression of these transcripts with RSEM. #I imported RSEM quantifications with tximport ...
deseq2 differential expression tximport rsem sequence length normalization written 3 months ago by al-ash10 • updated 3 months ago by Michael Love19k
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Comment: C: plotPCA - how to add labels to a PCA plot
... Thanks for pointing out ggrepel - I used the default geom_text_label which sufficiently solved in my case the overlapping labels but I will definitely give pcaExplorer a try. ...
written 20 months ago by al-ash10
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Comment: C: plotPCA - how to add labels to a PCA plot
... thanks! I used this approach in the end. ...
written 20 months ago by al-ash10
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plotPCA - how to add labels to a PCA plot
... I'm analyzing my HTseq count data using DEseq2 package. I generated the PCA plot using plotPCA(rld, intgroup="condition") Is there any straightforward way to label the points in a PCA plot by the names of the samples? (for example using a value named "sampleNames"). Thanks in advance! ...
deseq2 plotpca labels written 20 months ago by al-ash10 • updated 20 months ago by Federico Marini110

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Great Question 20 months ago, created a question with more than 5,000 views. For plotPCA - how to add labels to a PCA plot
Popular Question 20 months ago, created a question with more than 1,000 views. For plotPCA - how to add labels to a PCA plot

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